$ java -jar ${HOME}/programs/jvarkit/dist-2.0.1/samjs.jar -e 'function accept(rec) {if(rec.getReadUnmappedFlag()) return true; var c=rec.getCigar(); if(c==null) return true; for(var i=0;i< c.numCigarElements();++i) {var ce=c.getCigarElement(i);if(ce.getLength()<1000) continue;var s=ce.getOperator().name(); if( s=="D" ) return false; } return true;}accept(record)' Fasteris_Copenhagen_PlaquePurified_150903_SND104_B_L007_R1_HXE-3_mapped_NotPerfect_UnusedGeneiousLowSen_reBBmapped.sort.bam --samoutputformat SAM -X Fasteris_Copenhagen_PlaquePurified_150903_SND104_B_L007_R1_HXE-3_mapped_NotPerfect_UnusedGeneiousLowSen_reBBmapped.Indel-1000.sam -o Fasteris_Copenhagen_PlaquePurified_150903_SND104_B_L007_R1_HXE-3_mapped_NotPerfect_UnusedGeneiousLowSen_reBBmapped.noIndel-1000.sam
[main] ERROR jvarkit - Unknown command (--samoutputformat) , please check your input.
org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: --samoutputformat
	at org.apache.commons.cli.DefaultParser.handleUnknownToken(DefaultParser.java:347)
	at org.apache.commons.cli.DefaultParser.handleLongOptionWithoutEqual(DefaultParser.java:394)
	at org.apache.commons.cli.DefaultParser.handleLongOption(DefaultParser.java:371)
	at org.apache.commons.cli.DefaultParser.handleToken(DefaultParser.java:239)
	at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:120)
	at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:76)
	at org.apache.commons.cli.DefaultParser.parse(DefaultParser.java:60)
	at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExceptions(Command.java:476)
	at com.github.lindenb.jvarkit.util.command.Command.instanceMain(Command.java:570)
	at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExit(Command.java:576)
	at com.github.lindenb.jvarkit.tools.samjs.SamJavascript.main(SamJavascript.java:150)


java -jar ${HOME}/programs/jvarkit/dist-2.0.1/samjs.jar -e 'function accept(rec) {if(rec.getReadUnmappedFlag()) return true; var c=rec.getCigar(); if(c==null) return true; for(var i=0;i< c.numCigarElements();++i) {var ce=c.getCigarElement(i);if(ce.getLength()<1000) continue;var s=ce.getOperator().name(); if( s=="D" ) return false; } return true;}accept(record)' Fasteris_Copenhagen_PlaquePurified_150903_SND104_B_L007_R1_HXE-3_mapped_NotPerfect_UnusedGeneiousLowSen_reBBmapped.sort.bam -X Fasteris_Copenhagen_PlaquePurified_150903_SND104_B_L007_R1_HXE-3_mapped_NotPerfect_UnusedGeneiousLowSen_reBBmapped.Indel-1000.sam -o Fasteris_Copenhagen_PlaquePurified_150903_SND104_B_L007_R1_HXE-3_mapped_NotPerfect_UnusedGeneiousLowSen_reBBmapped.noIndel-1000.sam

[main] ERROR jvarkit - option -X: file Fasteris_Copenhagen_PlaquePurified_150903_SND104_B_L007_R1_HXE-3_mapped_NotPerfect_UnusedGeneiousLowSen_reBBmapped.Indel-1000.sam doesn't exists