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  1. 2015-04-14 09:41:42 +0200
  2.  
  3. make
  4. HTSDIR=/usr/local/opt/htslib/include
  5. HTSLIB=/usr/local/opt/htslib/lib/libhts.a
  6.  
  7. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_index.o bam_index.c
  8. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_plcmd.o bam_plcmd.c
  9. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o sam_view.o sam_view.c
  10. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_cat.o bam_cat.c
  11. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_md.o bam_md.c
  12. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_reheader.o bam_reheader.c
  13. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_sort.o bam_sort.c
  14. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bedidx.o bedidx.c
  15. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o kprobaln.o kprobaln.c
  16. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_rmdup.o bam_rmdup.c
  17. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_rmdupse.o bam_rmdupse.c
  18. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_mate.o bam_mate.c
  19. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_stat.o bam_stat.c
  20. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_color.o bam_color.c
  21. echo '#define SAMTOOLS_VERSION "1.2"' > version.h
  22. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam2bcf.o bam2bcf.c
  23. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam2bcf_indel.o bam2bcf_indel.c
  24. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o errmod.o errmod.c
  25. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o sample.o sample.c
  26. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o cut_target.o cut_target.c
  27. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o phase.o phase.c
  28. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam2depth.o bam2depth.c
  29. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o padding.o padding.c
  30. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bedcov.o bedcov.c
  31. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bamshuf.o bamshuf.c
  32. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o faidx.o faidx.c
  33. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o stats.o stats.c
  34. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o stats_isize.o stats_isize.c
  35. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_flags.o bam_flags.c
  36. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_split.o bam_split.c
  37. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_tview.o bam_tview.c
  38. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_tview_curses.o bam_tview_curses.c
  39. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_tview_html.o bam_tview_html.c
  40. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_lpileup.o bam_lpileup.c
  41. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_aux.o bam_aux.c
  42. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam.o bam.c
  43. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_import.o bam_import.c
  44. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o sam.o sam.c
  45. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o sam_header.o sam_header.c
  46. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bam_plbuf.o bam_plbuf.c
  47. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o misc/ace2sam.o misc/ace2sam.c
  48. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
  49. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o misc/maq2sam-short.o misc/maq2sam.c
  50. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o misc/md5fa.o misc/md5fa.c
  51. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o misc/md5.o misc/md5.c
  52. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
  53. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o misc/wgsim.o misc/wgsim.c
  54. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
  55. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o test/test.o test/test.c
  56. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
  57. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
  58. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
  59. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o test/split/test_count_rg.o test/split/test_count_rg.c
  60. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
  61. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
  62. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o test/split/test_parse_args.o test/split/test_parse_args.c
  63. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o test/vcf-miniview.o test/vcf-miniview.c
  64. gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/local/opt/htslib/include -c -o bamtk.o bamtk.c
  65. ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
  66. gcc -o misc/ace2sam misc/ace2sam.o -lz
  67. gcc -o misc/maq2sam-long misc/maq2sam-long.o -lz
  68. gcc -o misc/maq2sam-short misc/maq2sam-short.o -lz
  69. gcc -o misc/md5fa misc/md5fa.o misc/md5.o -lz
  70. gcc -o misc/md5sum-lite misc/md5sum-lite.o
  71. gcc -o misc/wgsim misc/wgsim.o -lm -lz
  72. gcc -pthread -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/local/opt/htslib/lib/libhts.a -lz
  73. gcc -pthread -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/local/opt/htslib/lib/libhts.a -lz
  74. gcc -pthread -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/local/opt/htslib/lib/libhts.a -lz
  75. gcc -pthread -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/local/opt/htslib/lib/libhts.a -lz
  76. gcc -pthread -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/local/opt/htslib/lib/libhts.a -lz
  77. gcc -pthread -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/local/opt/htslib/lib/libhts.a -lz
  78. gcc -pthread -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/local/opt/htslib/lib/libhts.a -lz
  79. gcc -pthread -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/local/opt/htslib/lib/libhts.a -lz
  80. gcc -pthread -o test/vcf-miniview test/vcf-miniview.o /usr/local/opt/htslib/lib/libhts.a -lz
  81. gcc -pthread -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/local/opt/htslib/lib/libhts.a -lcurses -lm -lz
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