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  1. make[1]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen'
  2. make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/samtools'
  3. ln -s ../samtools/bgzf.h ../include/bgzf.h
  4. ln -s ../samtools/knetfile.h ../include/knetfile.h
  5. ln -s ../samtools/khash.h ../include/khash.h
  6. ln -s ../samtools/bam.h ../include/bam.h
  7. mkdir -p obj
  8. gcc -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/bgzf.o -c bgzf.c
  9. gcc -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/knetfile.o -c knetfile.c
  10. ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o
  11. mkdir -p obj/debug
  12. gcc -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/bgzf.o -c bgzf.c
  13. gcc -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/knetfile.o -c knetfile.c
  14. ar -cru ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o
  15. mkdir -p obj/profile
  16. gcc -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/bgzf.o -c bgzf.c
  17. gcc -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/knetfile.o -c knetfile.c
  18. ar -cru ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o
  19. make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/samtools'
  20. make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/general'
  21. ln -s ../general/BaseAsciiMap.h ../include/BaseAsciiMap.h
  22. ln -s ../general/BaseQualityHelper.h ../include/BaseQualityHelper.h
  23. ln -s ../general/BaseUtilities.h ../include/BaseUtilities.h
  24. ln -s ../general/BasicHash.h ../include/BasicHash.h
  25. ln -s ../general/BgzfFileType.h ../include/BgzfFileType.h
  26. ln -s ../general/BgzfFileTypeRecovery.h ../include/BgzfFileTypeRecovery.h
  27. ln -s ../general/CharBuffer.h ../include/CharBuffer.h
  28. ln -s ../general/Chromosome.h ../include/Chromosome.h
  29. ln -s ../general/Cigar.h ../include/Cigar.h
  30. ln -s ../general/CigarRoller.h ../include/CigarRoller.h
  31. ln -s ../general/Error.h ../include/Error.h
  32. ln -s ../general/ErrorHandler.h ../include/ErrorHandler.h
  33. ln -s ../general/FileType.h ../include/FileType.h
  34. ln -s ../general/FortranFormat.h ../include/FortranFormat.h
  35. ln -s ../general/GenomeSequence.h ../include/GenomeSequence.h
  36. ln -s ../general/GenotypeLists.h ../include/GenotypeLists.h
  37. ln -s ../general/glfHandler.h ../include/glfHandler.h
  38. ln -s ../general/GzipFileType.h ../include/GzipFileType.h
  39. ln -s ../general/GzipHeader.h ../include/GzipHeader.h
  40. ln -s ../general/Hash.h ../include/Hash.h
  41. ln -s ../general/IndexBase.h ../include/IndexBase.h
  42. ln -s ../general/Input.h ../include/Input.h
  43. ln -s ../general/InputFile.h ../include/InputFile.h
  44. ln -s ../general/IntArray.h ../include/IntArray.h
  45. ln -s ../general/IntHash.h ../include/IntHash.h
  46. ln -s ../general/LongLongCounter.h ../include/LongLongCounter.h
  47. ln -s ../general/MapFunction.h ../include/MapFunction.h
  48. ln -s ../general/MathMatrix.h ../include/MathMatrix.h
  49. ln -s ../general/MathVector.h ../include/MathVector.h
  50. ln -s ../general/MemoryAllocators.h ../include/MemoryAllocators.h
  51. ln -s ../general/MemoryInfo.h ../include/MemoryInfo.h
  52. ln -s ../general/MemoryMapArray.h ../include/MemoryMapArray.h
  53. ln -s ../general/MemoryMap.h ../include/MemoryMap.h
  54. ln -s ../general/MiniDeflate.h ../include/MiniDeflate.h
  55. ln -s ../general/NonOverlapRegions.h ../include/NonOverlapRegions.h
  56. ln -s ../general/Parameters.h ../include/Parameters.h
  57. ln -s ../general/PedigreeAlleleFreq.h ../include/PedigreeAlleleFreq.h
  58. ln -s ../general/Pedigree.h ../include/Pedigree.h
  59. ln -s ../general/PedigreeDescription.h ../include/PedigreeDescription.h
  60. ln -s ../general/PedigreeFamily.h ../include/PedigreeFamily.h
  61. ln -s ../general/PedigreeGlobals.h ../include/PedigreeGlobals.h
  62. ln -s ../general/PedigreePerson.h ../include/PedigreePerson.h
  63. ln -s ../general/QuickIndex.h ../include/QuickIndex.h
  64. ln -s ../general/Random.h ../include/Random.h
  65. ln -s ../general/ReferenceSequence.h ../include/ReferenceSequence.h
  66. ln -s ../general/SmithWaterman.h ../include/SmithWaterman.h
  67. ln -s ../general/Sort.h ../include/Sort.h
  68. ln -s ../general/STLUtilities.h ../include/STLUtilities.h
  69. ln -s ../general/StatGenStatus.h ../include/StatGenStatus.h
  70. ln -s ../general/StringAlias.h ../include/StringAlias.h
  71. ln -s ../general/StringArray.h ../include/StringArray.h
  72. ln -s ../general/StringBasics.h ../include/StringBasics.h
  73. ln -s ../general/StringHash.h ../include/StringHash.h
  74. ln -s ../general/StringMap.h ../include/StringMap.h
  75. ln -s ../general/Tabix.h ../include/Tabix.h
  76. ln -s ../general/UncompressedFileType.h ../include/UncompressedFileType.h
  77. ln -s ../general/WindowsHelper.h ../include/WindowsHelper.h
  78. ln -s ../general/Constant.h ../include/Constant.h
  79. ln -s ../general/CSG_MD5.h ../include/CSG_MD5.h
  80. ln -s ../general/Generic.h ../include/Generic.h
  81. ln -s ../general/GenomeSequenceHelpers.h ../include/GenomeSequenceHelpers.h
  82. ln -s ../general/GreedyTupleAligner.h ../include/GreedyTupleAligner.h
  83. ln -s ../general/InplaceMerge.h ../include/InplaceMerge.h
  84. ln -s ../general/LongHash.h ../include/LongHash.h
  85. ln -s ../general/LongInt.h ../include/LongInt.h
  86. ln -s ../general/MathConstant.h ../include/MathConstant.h
  87. ln -s ../general/PackedVector.h ../include/PackedVector.h
  88. ln -s ../general/PedigreeAlleles.h ../include/PedigreeAlleles.h
  89. ln -s ../general/Performance.h ../include/Performance.h
  90. ln -s ../general/ReusableVector.h ../include/ReusableVector.h
  91. ln -s ../general/SimpleStats.h ../include/SimpleStats.h
  92. ln -s ../general/TrimSequence.h ../include/TrimSequence.h
  93. ln -s ../general/UnitTest.h ../include/UnitTest.h
  94. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\""
  95. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\""
  96. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\""
  97. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\""
  98. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\""
  99. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\""
  100. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\""
  101. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\""
  102. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\""
  103. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\""
  104. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Error.o -c Error.cpp -DVERSION="\"1.0.0\""
  105. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\""
  106. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\""
  107. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\""
  108. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\""
  109. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\""
  110. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\""
  111. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\""
  112. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\""
  113. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\""
  114. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\""
  115. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Input.o -c Input.cpp -DVERSION="\"1.0.0\""
  116. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\""
  117. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\""
  118. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\""
  119. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\""
  120. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\""
  121. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\""
  122. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\""
  123. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\""
  124. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\""
  125. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\""
  126. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\""
  127. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\""
  128. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\""
  129. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\""
  130. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\""
  131. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\""
  132. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\""
  133. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\""
  134. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\""
  135. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\""
  136. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\""
  137. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
  138. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\""
  139. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
  140. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\""
  141. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\""
  142. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
  143. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\""
  144. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
  145. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
  146. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
  147. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
  148. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
  149. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
  150. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/WindowsHelper.o -c WindowsHelper.cpp -DVERSION="\"1.0.0\""
  151. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
  152. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
  153. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
  154. ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/WindowsHelper.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o
  155. mkdir -p obj/debug
  156. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\""
  157. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\""
  158. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\""
  159. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\""
  160. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\""
  161. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\""
  162. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\""
  163. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\""
  164. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\""
  165. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\""
  166. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Error.o -c Error.cpp -DVERSION="\"1.0.0\""
  167. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\""
  168. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\""
  169. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\""
  170. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\""
  171. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\""
  172. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\""
  173. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\""
  174. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\""
  175. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\""
  176. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\""
  177. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Input.o -c Input.cpp -DVERSION="\"1.0.0\""
  178. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\""
  179. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\""
  180. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\""
  181. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\""
  182. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\""
  183. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\""
  184. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\""
  185. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\""
  186. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\""
  187. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\""
  188. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\""
  189. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\""
  190. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\""
  191. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\""
  192. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\""
  193. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\""
  194. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\""
  195. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\""
  196. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\""
  197. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\""
  198. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\""
  199. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
  200. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\""
  201. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
  202. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\""
  203. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\""
  204. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
  205. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\""
  206. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
  207. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
  208. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
  209. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
  210. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
  211. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
  212. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/WindowsHelper.o -c WindowsHelper.cpp -DVERSION="\"1.0.0\""
  213. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
  214. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
  215. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
  216. ar -cru ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/WindowsHelper.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o
  217. mkdir -p obj/profile
  218. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\""
  219. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\""
  220. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\""
  221. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\""
  222. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\""
  223. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\""
  224. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\""
  225. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\""
  226. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\""
  227. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\""
  228. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Error.o -c Error.cpp -DVERSION="\"1.0.0\""
  229. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\""
  230. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\""
  231. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\""
  232. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\""
  233. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\""
  234. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\""
  235. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\""
  236. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\""
  237. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\""
  238. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\""
  239. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Input.o -c Input.cpp -DVERSION="\"1.0.0\""
  240. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\""
  241. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\""
  242. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\""
  243. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\""
  244. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\""
  245. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\""
  246. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\""
  247. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\""
  248. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\""
  249. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\""
  250. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\""
  251. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\""
  252. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\""
  253. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\""
  254. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\""
  255. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\""
  256. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\""
  257. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\""
  258. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\""
  259. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\""
  260. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\""
  261. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
  262. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\""
  263. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
  264. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\""
  265. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\""
  266. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
  267. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\""
  268. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
  269. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
  270. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
  271. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
  272. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
  273. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
  274. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/WindowsHelper.o -c WindowsHelper.cpp -DVERSION="\"1.0.0\""
  275. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
  276. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
  277. g++ -pipe -Wall -Werror -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
  278. ar -cru ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/WindowsHelper.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o
  279. make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/general'
  280. make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/bam'
  281. ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h
  282. ln -s ../bam/SamFile.h ../include/SamFile.h
  283. ln -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h
  284. ln -s ../bam/SamInterface.h ../include/SamInterface.h
  285. ln -s ../bam/BamInterface.h ../include/BamInterface.h
  286. ln -s ../bam/SamRecord.h ../include/SamRecord.h
  287. ln -s ../bam/BamIndex.h ../include/BamIndex.h
  288. ln -s ../bam/SamHeaderHD.h ../include/SamHeaderHD.h
  289. ln -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h
  290. ln -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h
  291. ln -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h
  292. ln -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h
  293. ln -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h
  294. ln -s ../bam/SamValidation.h ../include/SamValidation.h
  295. ln -s ../bam/SamStatistics.h ../include/SamStatistics.h
  296. ln -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h
  297. ln -s ../bam/SamFilter.h ../include/SamFilter.h
  298. ln -s ../bam/PileupElement.h ../include/PileupElement.h
  299. ln -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h
  300. ln -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h
  301. ln -s ../bam/SamTags.h ../include/SamTags.h
  302. ln -s ../bam/PosList.h ../include/PosList.h
  303. ln -s ../bam/CigarHelper.h ../include/CigarHelper.h
  304. ln -s ../bam/SamRecordPool.h ../include/SamRecordPool.h
  305. ln -s ../bam/SamCoordOutput.h ../include/SamCoordOutput.h
  306. ln -s ../bam/SamRecordHelper.h ../include/SamRecordHelper.h
  307. ln -s ../bam/Pileup.h ../include/Pileup.h
  308. ln -s ../bam/SamHelper.h ../include/SamHelper.h
  309. ln -s ../bam/SamFlag.h ../include/SamFlag.h
  310. ln -s ../bam/SamStatus.h ../include/SamStatus.h
  311. mkdir -p obj
  312. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\""
  313. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\""
  314. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\""
  315. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\""
  316. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\""
  317. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\""
  318. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\""
  319. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\""
  320. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\""
  321. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\""
  322. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\""
  323. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\""
  324. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\""
  325. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\""
  326. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\""
  327. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\""
  328. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\""
  329. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\""
  330. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\""
  331. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\""
  332. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\""
  333. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\""
  334. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\""
  335. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\""
  336. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\""
  337. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\""
  338. ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o
  339. mkdir -p obj/debug
  340. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\""
  341. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\""
  342. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\""
  343. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\""
  344. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\""
  345. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\""
  346. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\""
  347. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\""
  348. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\""
  349. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\""
  350. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\""
  351. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\""
  352. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\""
  353. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\""
  354. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\""
  355. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\""
  356. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\""
  357. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\""
  358. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\""
  359. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\""
  360. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\""
  361. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\""
  362. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\""
  363. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\""
  364. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\""
  365. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\""
  366. ar -cru ../libStatGen_debug.a obj/debug/SamFileHeader.o obj/debug/SamFile.o obj/debug/GenericSamInterface.o obj/debug/SamInterface.o obj/debug/BamInterface.o obj/debug/SamRecord.o obj/debug/BamIndex.o obj/debug/SamHeaderHD.o obj/debug/SamHeaderPG.o obj/debug/SamHeaderRecord.o obj/debug/SamHeaderSQ.o obj/debug/SamHeaderRG.o obj/debug/SamHeaderTag.o obj/debug/SamValidation.o obj/debug/SamStatistics.o obj/debug/SamQuerySeqWithRefHelper.o obj/debug/SamFilter.o obj/debug/PileupElement.o obj/debug/PileupElementBaseQual.o obj/debug/SamReferenceInfo.o obj/debug/SamTags.o obj/debug/PosList.o obj/debug/CigarHelper.o obj/debug/SamRecordPool.o obj/debug/SamCoordOutput.o obj/debug/SamRecordHelper.o
  367. mkdir -p obj/profile
  368. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\""
  369. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\""
  370. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\""
  371. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\""
  372. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\""
  373. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\""
  374. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\""
  375. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\""
  376. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\""
  377. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\""
  378. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\""
  379. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\""
  380. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\""
  381. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\""
  382. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\""
  383. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\""
  384. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\""
  385. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\""
  386. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\""
  387. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\""
  388. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\""
  389. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\""
  390. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\""
  391. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\""
  392. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\""
  393. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\""
  394. ar -cru ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o
  395. make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/bam'
  396. make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/fastq'
  397. ln -s ../fastq/FastQFile.h ../include/FastQFile.h
  398. ln -s ../fastq/BaseCount.h ../include/BaseCount.h
  399. ln -s ../fastq/BaseComposition.h ../include/BaseComposition.h
  400. ln -s ../fastq/FastQStatus.h ../include/FastQStatus.h
  401. mkdir -p obj
  402. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\""
  403. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\""
  404. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\""
  405. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\""
  406. ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o
  407. mkdir -p obj/debug
  408. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\""
  409. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\""
  410. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\""
  411. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\""
  412. ar -cru ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o
  413. mkdir -p obj/profile
  414. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\""
  415. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\""
  416. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\""
  417. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\""
  418. ar -cru ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o
  419. make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/fastq'
  420. make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/glf'
  421. ln -s ../glf/GlfException.h ../include/GlfException.h
  422. ln -s ../glf/GlfFile.h ../include/GlfFile.h
  423. ln -s ../glf/GlfHeader.h ../include/GlfHeader.h
  424. ln -s ../glf/GlfRecord.h ../include/GlfRecord.h
  425. ln -s ../glf/GlfRefSection.h ../include/GlfRefSection.h
  426. ln -s ../glf/GlfStatus.h ../include/GlfStatus.h
  427. mkdir -p obj
  428. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\""
  429. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\""
  430. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\""
  431. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\""
  432. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\""
  433. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\""
  434. ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
  435. mkdir -p obj/debug
  436. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\""
  437. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\""
  438. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\""
  439. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\""
  440. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\""
  441. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\""
  442. ar -cru ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o
  443. mkdir -p obj/profile
  444. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\""
  445. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\""
  446. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\""
  447. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\""
  448. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\""
  449. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\""
  450. ar -cru ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o
  451. make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/glf'
  452. make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/vcf'
  453. ln -s ../vcf/VcfFile.h ../include/VcfFile.h
  454. ln -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h
  455. ln -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h
  456. ln -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h
  457. ln -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h
  458. ln -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h
  459. ln -s ../vcf/VcfHeader.h ../include/VcfHeader.h
  460. ln -s ../vcf/VcfHelper.h ../include/VcfHelper.h
  461. ln -s ../vcf/VcfRecord.h ../include/VcfRecord.h
  462. ln -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h
  463. ln -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h
  464. ln -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.h
  465. ln -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h
  466. ln -s ../vcf/VcfSubsetSamples.h ../include/VcfSubsetSamples.h
  467. mkdir -p obj
  468. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\""
  469. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\""
  470. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\""
  471. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\""
  472. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\""
  473. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\""
  474. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\""
  475. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\""
  476. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\""
  477. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\""
  478. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\""
  479. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\""
  480. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\""
  481. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\""
  482. ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o
  483. mkdir -p obj/debug
  484. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\""
  485. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\""
  486. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\""
  487. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\""
  488. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\""
  489. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\""
  490. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\""
  491. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\""
  492. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\""
  493. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\""
  494. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\""
  495. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\""
  496. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\""
  497. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\""
  498. ar -cru ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o
  499. mkdir -p obj/profile
  500. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\""
  501. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\""
  502. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\""
  503. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\""
  504. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\""
  505. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\""
  506. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\""
  507. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\""
  508. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\""
  509. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\""
  510. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\""
  511. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\""
  512. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\""
  513. g++ -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\""
  514. ar -cru ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o
  515. make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/vcf'
  516. make[1]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen'
  517. mkdir --p lib/
  518. cd lib/; ln -s ../libStatGen/libStatGen.a libStatGen.a; cd ..
  519. make[1]: Entering directory `/home/daithanh/Learning/1000genomes/umake/samtools-hybrid'
  520. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bgzf.c -o bgzf.o
  521. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 kstring.c -o kstring.o
  522. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_aux.c -o bam_aux.o
  523. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam.c -o bam.o
  524. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_import.c -o bam_import.o
  525. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 sam.c -o sam.o
  526. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_index.c -o bam_index.o
  527. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_pileup.c -o bam_pileup.o
  528. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_lpileup.c -o bam_lpileup.o
  529. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_md.c -o bam_md.o
  530. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 glf.c -o glf.o
  531. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 razf.c -o razf.o
  532. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 faidx.c -o faidx.o
  533. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 knetfile.c -o knetfile.o
  534. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_sort.c -o bam_sort.o
  535. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 sam_header.c -o sam_header.o
  536. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 kprobaln.c -o kprobaln.o
  537. ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o kprobaln.o
  538. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_tview.c -o bam_tview.o
  539. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_maqcns.c -o bam_maqcns.o
  540. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_plcmd.c -o bam_plcmd.o
  541. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 sam_view.c -o sam_view.o
  542. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_rmdup.c -o bam_rmdup.o
  543. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_rmdupse.c -o bam_rmdupse.o
  544. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_mate.c -o bam_mate.o
  545. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_stat.c -o bam_stat.o
  546. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bam_color.c -o bam_color.o
  547. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 bamtk.c -o bamtk.o
  548. gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 kaln.c -o kaln.o
  549. mkdir --p bin/
  550. gcc -g -Wall -O2 -o bin/samtools-hybrid bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o -lm -lcurses -L. -lbam -lz
  551. make[1]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/samtools-hybrid'
  552. mkdir --p bin/
  553. cd bin/; ln -s ../samtools-hybrid/bin/samtools-hybrid samtools-hybrid; cd ..
  554. make[1]: Entering directory `/home/daithanh/Learning/1000genomes/umake/glfExtract'
  555. make -C ../libStatGen --no-print-directory opt
  556. ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o
  557. ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/WindowsHelper.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o
  558. ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o
  559. ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o
  560. ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
  561. ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o
  562. mkdir -p ../obj
  563. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:53 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../obj/GlfLikelihoods.o -c GlfLikelihoods.cpp -DVERSION="\"0.1.1\""
  564. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:53 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../obj/MathGold.o -c MathGold.cpp -DVERSION="\"0.1.1\""
  565. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:54 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../obj/Main.o -c Main.cpp -DVERSION="\"0.1.1\""
  566. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:54 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../bin/glfExtract ../obj/GlfLikelihoods.o ../obj/MathGold.o ../obj/Main.o ../libStatGen/libStatGen.a -lm -lz
  567. mkdir -p ../bin/debug
  568. make -C ../libStatGen --no-print-directory debug
  569. ar -cru ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o
  570. ar -cru ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/WindowsHelper.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o
  571. ar -cru ../libStatGen_debug.a obj/debug/SamFileHeader.o obj/debug/SamFile.o obj/debug/GenericSamInterface.o obj/debug/SamInterface.o obj/debug/BamInterface.o obj/debug/SamRecord.o obj/debug/BamIndex.o obj/debug/SamHeaderHD.o obj/debug/SamHeaderPG.o obj/debug/SamHeaderRecord.o obj/debug/SamHeaderSQ.o obj/debug/SamHeaderRG.o obj/debug/SamHeaderTag.o obj/debug/SamValidation.o obj/debug/SamStatistics.o obj/debug/SamQuerySeqWithRefHelper.o obj/debug/SamFilter.o obj/debug/PileupElement.o obj/debug/PileupElementBaseQual.o obj/debug/SamReferenceInfo.o obj/debug/SamTags.o obj/debug/PosList.o obj/debug/CigarHelper.o obj/debug/SamRecordPool.o obj/debug/SamCoordOutput.o obj/debug/SamRecordHelper.o
  572. ar -cru ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o
  573. ar -cru ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o
  574. ar -cru ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o
  575. mkdir -p ../obj/debug
  576. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:54 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../obj/debug/GlfLikelihoods.o -c GlfLikelihoods.cpp -DVERSION="\"0.1.1\""
  577. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:55 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../obj/debug/MathGold.o -c MathGold.cpp -DVERSION="\"0.1.1\""
  578. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:55 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../obj/debug/Main.o -c Main.cpp -DVERSION="\"0.1.1\""
  579. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:56 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../bin/debug/glfExtract ../obj/debug/GlfLikelihoods.o ../obj/debug/MathGold.o ../obj/debug/Main.o ../libStatGen/libStatGen_debug.a -lm -lz
  580. mkdir -p ../bin/profile
  581. make -C ../libStatGen --no-print-directory profile
  582. ar -cru ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o
  583. ar -cru ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/WindowsHelper.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o
  584. ar -cru ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o
  585. ar -cru ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o
  586. ar -cru ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o
  587. ar -cru ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o
  588. mkdir -p ../obj/profile
  589. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:56 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../obj/profile/GlfLikelihoods.o -c GlfLikelihoods.cpp -DVERSION="\"0.1.1\""
  590. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:56 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../obj/profile/MathGold.o -c MathGold.cpp -DVERSION="\"0.1.1\""
  591. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:57 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../obj/profile/Main.o -c Main.cpp -DVERSION="\"0.1.1\""
  592. g++ -pipe -Wall -I../libStatGen/include -I. -I../include/ -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:57 ICT\"" -DVERSION="\"0.1.1\"" -DUSER="\"daithanh\"" -lcrypto -o ../bin/profile/glfExtract ../obj/profile/GlfLikelihoods.o ../obj/profile/MathGold.o ../obj/profile/Main.o ../libStatGen/libStatGen_profile.a -lm -lz
  593. make[1]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/glfExtract'
  594. mkdir --p bin/
  595. cd bin/; ln -s ../glfExtract/bin/glfExtract glfExtract; cd ..
  596. make[1]: Entering directory `/home/daithanh/Learning/1000genomes/umake/glfMerge'
  597. make -C ../libStatGen --no-print-directory opt
  598. ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o
  599. ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/WindowsHelper.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o
  600. ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o
  601. ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o
  602. ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
  603. ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o
  604. g++ -pipe -Wall -I../libStatGen/include -I. -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -DDATE="\"Thứ ba, 25 Tháng sáu năm 2013 22:54:57 ICT\"" -DVERSION="\"1.0.0\"" -DUSER="\"daithanh\"" -lcrypto -o ../bin/glfMerge ../obj/Main.o ../libStatGen/libStatGen.a -lm -lz
  605. make[1]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/glfMerge'
  606. bgzf.c: In function ‘bgzf_close’:
  607. bgzf.c:587:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
  608. bam_index.c: In function ‘bam_index_load_core’:
  609. bam_index.c:276:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  610. bam_index.c:283:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  611. bam_index.c:296:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  612. bam_index.c:299:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  613. bam_index.c:303:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  614. bam_index.c:307:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  615. bam_index.c:317:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  616. bam_index.c:321:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  617. razf.c: In function ‘razf_close’:
  618. razf.c:804:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  619. razf.c:805:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  620. razf.c:808:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  621. razf.c:810:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  622. razf.c: In function ‘razf_end_flush’:
  623. razf.c:258:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  624. razf.c: In function ‘_razf_write’:
  625. razf.c:201:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  626. razf.c: In function ‘save_zindex’:
  627. razf.c:96:17: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  628. razf.c:99:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  629. razf.c:106:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  630. razf.c:107:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  631. razf.c: In function ‘razf_flush’:
  632. razf.c:221:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  633. razf.c:234:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  634. knetfile.c: In function ‘khttp_connect_file’:
  635. knetfile.c:416:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  636. knetfile.c: In function ‘kftp_send_cmd’:
  637. knetfile.c:237:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  638. kprobaln.c: In function ‘kpa_glocal’:
  639. kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
  640. ln: failed to create symbolic link ‘glfExtract’: File exists
  641. ../obj/Main.o: In function `ReportGenotypes(GenotypeLikelihood&, glfHandler*, int, int, int, int, int, String&, String&)':
  642. Main.cpp:(.text+0x35c): undefined reference to `GenotypeLikelihood::GetFemalePriors(double*, double)'
  643. Main.cpp:(.text+0x37e): undefined reference to `GenotypeLikelihood::GetMalePriors(double*, double)'
  644. ../obj/Main.o: In function `ReportSNP(GenotypeLikelihood&, int, int, int, int, int, char const*, int, int, double)':
  645. Main.cpp:(.text+0x14e6): undefined reference to `GenotypeLikelihood::SetAlleles(int, int)'
  646. Main.cpp:(.text+0x14f1): undefined reference to `GenotypeLikelihood::OptimizeFrequency()'
  647. ../obj/Main.o: In function `main':
  648. Main.cpp:(.text+0x2292): undefined reference to `GenotypeLikelihood::GenotypeLikelihood(int, glfHandler*)'
  649. Main.cpp:(.text+0x2a31): undefined reference to `GenotypeLikelihood::~GenotypeLikelihood()'
  650. Main.cpp:(.text+0x2bcc): undefined reference to `GenotypeLikelihood::~GenotypeLikelihood()'
  651. collect2: error: ld returned 1 exit status
  652. make[1]: *** [../bin/glfMerge] Error 1
  653. make: *** [glfMerge] Error 2
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