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Setup:
$ BAM2SAM="@PacBioBAM_BinDir@/bam2sam" && export BAM2SAM
$ DATADIR="@PacBioBAM_TestsDir@/data" && export DATADIR
Normal:
$ $BAM2SAM < $DATADIR/phi29.bam | head -n 5
@HD\tVN:3.0.0\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:a955def6\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;Ipd:CodecV1=ip;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3.0.0.140018;FRAMERATEHZ=75.000000\tPU:m140918_150013_42139_c100697631700000001823144703261565_s1_p0 (esc)
@PG\tID:bam2bam-0.20.0\tPN:bam2bam\tVN:0.20.0 (esc)
@PG\tID:bax2bam-0.0.2\tPN:bax2bam\tVN:0.0.2 (esc)
m140918_150013_42139_c100697631700000001823144703261565_s1_p0/30422/2067_4072\t4\t*\t0\t255\t*\t*\t0\t0\tAAGTCATGTATAGAGTTATTGGCTCAGCGGTGGCAAGCAGCCAACTCAGCTCCTTTCGGGCTTGTTAGCAGCCGGATCCACACTCTGAAATTCCTGCAGCTCGAGTTATTTGATAGTAAAAGTGGGTCATCAAACCGCAACTACGCCACCCCGGTACCTGAACAGGCTTCGGTTTCATTTTGAGACGAGAAAAACCCACTTTGAAGTTTTCGAAAATCACTTCCTTTTTTGATTTTGTCCGTCATGCCTGCGCATTTCACAAGAGAACTTGATGTCAGTGTTAGTCGTCAGGAGAGCCTCTACCAGTTTGCCGTCTACTTCTTTCATGTAAATATCCTGGATGTAAGGTTTTCTGACGCAGATATTGTTGGCAACGCTTAAAAAGTGGGATTCGTGTGGCCAGTAGCCCAGGTTATCTTTCGGGTCCACGATGTCTTTGATAACGTCCAGAATTTCAGTACCAGTTCAGGTGAATAGAACGGTATCGCAGTTTCAGATAATACGATCATGACAGCCTGCGCTGGCTGTGATGGTCGTATAGCGTGCCCAGGCCGTGATAAAGACACCCATCCGGGGTATATACAGGGTCTTTCGTTTCCTCCCTAGCCTAAGAAAGAAAACCCAGAGCACCGTTCTCTTCAAGGTATGGCACTTTACCGTAACGTCCGGGTTGGAAAGCGAAATTTACCGTACAGGCCTGGTTCAGCATCAGCTTCCCGCCAGCTGTTTGATGGCGTCCCTTCAGAGGTAGTTTTGATATACGTCCATTTTGTCGATAAAGTCCTTGAACAGGCAAGTGGTTCCTTTGAAACTTCAGACCAAGAGGATAATATTCAACATTGTACAGGTCGTAGTGTCTTTCATCAGTTCCAGATCAAACATTAGAACAGCCACAAGGTCAGCAAATTTCACCGCCGGAAGATTTCAGGTAATTCGTTACGCTTGTAAAGAAATTGGGACGCTTGATCTGGGATGGTCGGGATCTAGCCTCCTTCAGTTCAAATTCACTTAACGAATGTGCTGAATGTGCCAGAGGGTAATCCTCGTCCAAAGACGGTATTTACCCTCGAAACGATCGGCTCGCCGTACGGCAACGCAGGCGAGAGTACATTCTGCAGCTGGGTACAGGGAATTAAACATCAAAAACCATACCTTCGCCGATCTCTTTTTCCTTTAAAACGTCATTCAGCCACGGTGAAGACCAACCACGGTAAGGCATAACGAACTTCCTTGTCCAGACCCAGGCTCAGGGTCCGGGAAAACCTTTTTAAACTTCTTGTGGTGATAATGTCTTTGAAGCCTTTCAGAAGTCAGAACCTGCCGTCATACGATCCAAGACCACTGCTTGAACCTGGATCAGCAGACTTCTGCGATAATCTGAATATCGTTTTTAATGTAGGCAATATTTCTTCCGGGTGATTTTGTAACCGACCGGGCGCTCATTATGATAAGTCGATGTCGCCTTTCAGTAGCCGTCAGTTAAAAGTCTTTCGCAATTTTCTTAACGCGGAAAGGCAAGTTTCTAGAGAGTCGTAAGATCACGTGTGGAATCTTGCGTTTACCCTTGTAACCCAGGCAATACAATCATATAACCACTGGCCCAATGCGAGAAATGATGGTGTTGTAGGTATTTTGGCAGACCATCTGCGGACCGCATTTAAAACGTTACGTTCCAGCCAGTTGATGATGAAATGCGCCATCAAAATTTCAGATTTGTGGAAGTACAGGTCCCAGCCTGAAAACTTTGCAGAAACCCAAGCCATAAAATTCATCCAGGGAGTTACCAATCTTATACTCGGAGTGGTCTTCGATGTTCATTGTAACCGTATGCCCATACGCGGCAATCTTCAAGCCTTGGTGTAGTCTCAAAGTCGCAGGAATACATTTACGTGGCATGTGTTTCATATGTCATTCCTTCTTAAAGTTAAACAAAATTATTTCTAGAGGGGAATTGTTTATCCGCCTCACATTTCCCTATAGTGAGTCGTATTAATTTCGCGGGATC\t*\tRG:Z:a955def6\tbc:B:S,1,1\tbq:i:1\tcx:i:31\tnp:i:1\tqe:i:4072\tqs:i:2067\trq:f:0.88458\tsn:B:f,22.8448,13.8689,14.6461,14.3552\tzm:i:30422 (esc)
Explicit Filename (not stdin):
$ $BAM2SAM $DATADIR/phi29.bam | head -n 5
@HD\tVN:3.0.0\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:a955def6\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;Ipd:CodecV1=ip;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3.0.0.140018;FRAMERATEHZ=75.000000\tPU:m140918_150013_42139_c100697631700000001823144703261565_s1_p0 (esc)
@PG\tID:bam2bam-0.20.0\tPN:bam2bam\tVN:0.20.0 (esc)
@PG\tID:bax2bam-0.0.2\tPN:bax2bam\tVN:0.0.2 (esc)
m140918_150013_42139_c100697631700000001823144703261565_s1_p0/30422/2067_4072\t4\t*\t0\t255\t*\t*\t0\t0\tAAGTCATGTATAGAGTTATTGGCTCAGCGGTGGCAAGCAGCCAACTCAGCTCCTTTCGGGCTTGTTAGCAGCCGGATCCACACTCTGAAATTCCTGCAGCTCGAGTTATTTGATAGTAAAAGTGGGTCATCAAACCGCAACTACGCCACCCCGGTACCTGAACAGGCTTCGGTTTCATTTTGAGACGAGAAAAACCCACTTTGAAGTTTTCGAAAATCACTTCCTTTTTTGATTTTGTCCGTCATGCCTGCGCATTTCACAAGAGAACTTGATGTCAGTGTTAGTCGTCAGGAGAGCCTCTACCAGTTTGCCGTCTACTTCTTTCATGTAAATATCCTGGATGTAAGGTTTTCTGACGCAGATATTGTTGGCAACGCTTAAAAAGTGGGATTCGTGTGGCCAGTAGCCCAGGTTATCTTTCGGGTCCACGATGTCTTTGATAACGTCCAGAATTTCAGTACCAGTTCAGGTGAATAGAACGGTATCGCAGTTTCAGATAATACGATCATGACAGCCTGCGCTGGCTGTGATGGTCGTATAGCGTGCCCAGGCCGTGATAAAGACACCCATCCGGGGTATATACAGGGTCTTTCGTTTCCTCCCTAGCCTAAGAAAGAAAACCCAGAGCACCGTTCTCTTCAAGGTATGGCACTTTACCGTAACGTCCGGGTTGGAAAGCGAAATTTACCGTACAGGCCTGGTTCAGCATCAGCTTCCCGCCAGCTGTTTGATGGCGTCCCTTCAGAGGTAGTTTTGATATACGTCCATTTTGTCGATAAAGTCCTTGAACAGGCAAGTGGTTCCTTTGAAACTTCAGACCAAGAGGATAATATTCAACATTGTACAGGTCGTAGTGTCTTTCATCAGTTCCAGATCAAACATTAGAACAGCCACAAGGTCAGCAAATTTCACCGCCGGAAGATTTCAGGTAATTCGTTACGCTTGTAAAGAAATTGGGACGCTTGATCTGGGATGGTCGGGATCTAGCCTCCTTCAGTTCAAATTCACTTAACGAATGTGCTGAATGTGCCAGAGGGTAATCCTCGTCCAAAGACGGTATTTACCCTCGAAACGATCGGCTCGCCGTACGGCAACGCAGGCGAGAGTACATTCTGCAGCTGGGTACAGGGAATTAAACATCAAAAACCATACCTTCGCCGATCTCTTTTTCCTTTAAAACGTCATTCAGCCACGGTGAAGACCAACCACGGTAAGGCATAACGAACTTCCTTGTCCAGACCCAGGCTCAGGGTCCGGGAAAACCTTTTTAAACTTCTTGTGGTGATAATGTCTTTGAAGCCTTTCAGAAGTCAGAACCTGCCGTCATACGATCCAAGACCACTGCTTGAACCTGGATCAGCAGACTTCTGCGATAATCTGAATATCGTTTTTAATGTAGGCAATATTTCTTCCGGGTGATTTTGTAACCGACCGGGCGCTCATTATGATAAGTCGATGTCGCCTTTCAGTAGCCGTCAGTTAAAAGTCTTTCGCAATTTTCTTAACGCGGAAAGGCAAGTTTCTAGAGAGTCGTAAGATCACGTGTGGAATCTTGCGTTTACCCTTGTAACCCAGGCAATACAATCATATAACCACTGGCCCAATGCGAGAAATGATGGTGTTGTAGGTATTTTGGCAGACCATCTGCGGACCGCATTTAAAACGTTACGTTCCAGCCAGTTGATGATGAAATGCGCCATCAAAATTTCAGATTTGTGGAAGTACAGGTCCCAGCCTGAAAACTTTGCAGAAACCCAAGCCATAAAATTCATCCAGGGAGTTACCAATCTTATACTCGGAGTGGTCTTCGATGTTCATTGTAACCGTATGCCCATACGCGGCAATCTTCAAGCCTTGGTGTAGTCTCAAAGTCGCAGGAATACATTTACGTGGCATGTGTTTCATATGTCATTCCTTCTTAAAGTTAAACAAAATTATTTCTAGAGGGGAATTGTTTATCCGCCTCACATTTCCCTATAGTGAGTCGTATTAATTTCGCGGGATC\t*\tRG:Z:a955def6\tbc:B:S,1,1\tbq:i:1\tcx:i:31\tnp:i:1\tqe:i:4072\tqs:i:2067\trq:f:0.88458\tsn:B:f,22.8448,13.8689,14.6461,14.3552\tzm:i:30422 (esc)
Header-Only:
$ $BAM2SAM --header-only < $DATADIR/phi29.bam | head -n 5
@HD\tVN:3.0.0\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:a955def6\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;Ipd:CodecV1=ip;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3.0.0.140018;FRAMERATEHZ=75.000000\tPU:m140918_150013_42139_c100697631700000001823144703261565_s1_p0 (esc)
@PG\tID:bam2bam-0.20.0\tPN:bam2bam\tVN:0.20.0 (esc)
@PG\tID:bax2bam-0.0.2\tPN:bax2bam\tVN:0.0.2 (esc)
No-Header:
$ $BAM2SAM --no-header < $DATADIR/phi29.bam | head -n 5
m140918_150013_42139_c100697631700000001823144703261565_s1_p0/30422/2067_4072\t4\t*\t0\t255\t*\t*\t0\t0\tAAGTCATGTATAGAGTTATTGGCTCAGCGGTGGCAAGCAGCCAACTCAGCTCCTTTCGGGCTTGTTAGCAGCCGGATCCACACTCTGAAATTCCTGCAGCTCGAGTTATTTGATAGTAAAAGTGGGTCATCAAACCGCAACTACGCCACCCCGGTACCTGAACAGGCTTCGGTTTCATTTTGAGACGAGAAAAACCCACTTTGAAGTTTTCGAAAATCACTTCCTTTTTTGATTTTGTCCGTCATGCCTGCGCATTTCACAAGAGAACTTGATGTCAGTGTTAGTCGTCAGGAGAGCCTCTACCAGTTTGCCGTCTACTTCTTTCATGTAAATATCCTGGATGTAAGGTTTTCTGACGCAGATATTGTTGGCAACGCTTAAAAAGTGGGATTCGTGTGGCCAGTAGCCCAGGTTATCTTTCGGGTCCACGATGTCTTTGATAACGTCCAGAATTTCAGTACCAGTTCAGGTGAATAGAACGGTATCGCAGTTTCAGATAATACGATCATGACAGCCTGCGCTGGCTGTGATGGTCGTATAGCGTGCCCAGGCCGTGATAAAGACACCCATCCGGGGTATATACAGGGTCTTTCGTTTCCTCCCTAGCCTAAGAAAGAAAACCCAGAGCACCGTTCTCTTCAAGGTATGGCACTTTACCGTAACGTCCGGGTTGGAAAGCGAAATTTACCGTACAGGCCTGGTTCAGCATCAGCTTCCCGCCAGCTGTTTGATGGCGTCCCTTCAGAGGTAGTTTTGATATACGTCCATTTTGTCGATAAAGTCCTTGAACAGGCAAGTGGTTCCTTTGAAACTTCAGACCAAGAGGATAATATTCAACATTGTACAGGTCGTAGTGTCTTTCATCAGTTCCAGATCAAACATTAGAACAGCCACAAGGTCAGCAAATTTCACCGCCGGAAGATTTCAGGTAATTCGTTACGCTTGTAAAGAAATTGGGACGCTTGATCTGGGATGGTCGGGATCTAGCCTCCTTCAGTTCAAATTCACTTAACGAATGTGCTGAATGTGCCAGAGGGTAATCCTCGTCCAAAGACGGTATTTACCCTCGAAACGATCGGCTCGCCGTACGGCAACGCAGGCGAGAGTACATTCTGCAGCTGGGTACAGGGAATTAAACATCAAAAACCATACCTTCGCCGATCTCTTTTTCCTTTAAAACGTCATTCAGCCACGGTGAAGACCAACCACGGTAAGGCATAACGAACTTCCTTGTCCAGACCCAGGCTCAGGGTCCGGGAAAACCTTTTTAAACTTCTTGTGGTGATAATGTCTTTGAAGCCTTTCAGAAGTCAGAACCTGCCGTCATACGATCCAAGACCACTGCTTGAACCTGGATCAGCAGACTTCTGCGATAATCTGAATATCGTTTTTAATGTAGGCAATATTTCTTCCGGGTGATTTTGTAACCGACCGGGCGCTCATTATGATAAGTCGATGTCGCCTTTCAGTAGCCGTCAGTTAAAAGTCTTTCGCAATTTTCTTAACGCGGAAAGGCAAGTTTCTAGAGAGTCGTAAGATCACGTGTGGAATCTTGCGTTTACCCTTGTAACCCAGGCAATACAATCATATAACCACTGGCCCAATGCGAGAAATGATGGTGTTGTAGGTATTTTGGCAGACCATCTGCGGACCGCATTTAAAACGTTACGTTCCAGCCAGTTGATGATGAAATGCGCCATCAAAATTTCAGATTTGTGGAAGTACAGGTCCCAGCCTGAAAACTTTGCAGAAACCCAAGCCATAAAATTCATCCAGGGAGTTACCAATCTTATACTCGGAGTGGTCTTCGATGTTCATTGTAACCGTATGCCCATACGCGGCAATCTTCAAGCCTTGGTGTAGTCTCAAAGTCGCAGGAATACATTTACGTGGCATGTGTTTCATATGTCATTCCTTCTTAAAGTTAAACAAAATTATTTCTAGAGGGGAATTGTTTATCCGCCTCACATTTCCCTATAGTGAGTCGTATTAATTTCGCGGGATC\t*\tRG:Z:a955def6\tbc:B:S,1,1\tbq:i:1\tcx:i:31\tnp:i:1\tqe:i:4072\tqs:i:2067\trq:f:0.88458\tsn:B:f,22.8448,13.8689,14.6461,14.3552\tzm:i:30422 (esc)
m140918_150013_42139_c100697631700000001823144703261565_s1_p0/30422/4151_6183\t4\t*\t0\t255\t*\t*\t0\t0\tGATCCCGCGAATTAATTACGACTCACTATAGGGGAATTGTGAGCGGATAACAATTCCCGCCTCTAGAAATAATTTTGTTTAAACTTTTAAGAAAGGAGATATTACATATGAAACACAGCCACGTAAAATGTATTCCTGCGACTTGGAGACTACCACCAAGGTGAAGATTTGCCGCGTAATGGGCATACGGTTTACATGAAACATCGAAGAACAAACTCGAGTATAAGATTGGTAACTCCCCTGGATGAATTATGGCTTGGGTTACTGAAAGTTCGAGGTCTGACCTGTACTTCGCACAAATCTGAAAATTTGATGGCCGCAAATTTCAATTCATCACTGGCTGGAACGTAAACGGTTTTAAATGGTCCGCAGATCGGTCTGTGCCAAATACCCTGATCAACACATCATTTCTTCGCAATGCGGCCAGTGTAATGATTGATATCTTGCCCTGGGTTGACAAGGGGTAAACGCAAGATCCACACCTGTGATCTACGACCTCTCTGAAGAAAACTGCGTTTCCGGTTAAGAAAATTGCGAAAGACTTTAAGCTGAACGGTACTGAAAAGCGACATGACTATCATAATGAGCGCCCGGTCGTTACAAAATCACCCCGGAAAGAATATGCCTACATTTAAAAACGATATTCAGATTATCGCAAGAACTCTGCTGATCAGTTCAAGCAAGGGTCTGGATCGTAAATGACGGCAGGTTCTGACTCTCCTGAAAGGCTTCAAAAGACATTATCACCACCTAAAAGAAGTTTAAAAAGGTTTTTTCACCGACCCTGAGCCTAGGGCTGGACAAGGAAAGTTGTTAATGCCCATACCGTGGTGGTTTCACCTGGCTGAAAGACCGTTTTAAAGAAAAAGAGATCGGCGAAGGTATGGTTTTTGATGTTAATTCCCTGTAACCAAGCCTTCAATGTACTCTCGCCTGCTTGCCGTCACACGGGCGAGCGACGTATTCGAAAGGGTAAAATACGTTCTGGGACGGAGGATTTACCCTCTGCAATTCGGCACATTCCGTTGTGAATTTGGAACTGAAAGGAAGGCTTAGATCCCGACCATCCCAGATCAAGCGTTCCCATTTCTAACAAAGGGTAACGAATACCTGAAATCTTCCAGGCGGTGAAATTGCTGACCTGTGGCTGTCTAAATGTTTGATCTTGGAAACTGATGAAAGAGCACTACGACCTGGTACAATGTTGAATATATCTCTGGTCTGAAGTTCAAAGCAACCACTGGCCTGTTCAAGGACTTTATCGACAATGGACGTATATCAAAAGACTACCTCTGAAGACGCCATCAAACAGCTGGCGAAGCTGATGCTGACAAGCCTGTACGGTAAATTCGCGTCCCACCCGGACGTTTACCGGGTAAAGTGCCATATGCTGAAAGAGAAAGCGGTGCTCTGGTTTTTCGTCTAGGTGGAAGGAGGAAACGAAGACACTGTATATACCGCCGAATGGGTGTCTTTATCCAAGCGGCCTGGCACGCTATACGACCATCACAGGCAAGCGCAGGCTTTTGTTAATGATCGTATTATCTACTGCGATTACCGATTCTACTTCACTGACTGGTACTGAAATCTGGACGTTATCAAAGACATCGTAGACCCGAAGAAACTGGGCTACTGGCACACGAATTCCACTTTAAGCGTGCAAAATATCTGCGTCAGAAAACCTACATCCCAGGATATTTACATGAAAGAAGTAGACGGCAAACTGGTAGAGGGCTCTCCGTGACGACTACACTGACATCAAGTTCTCTGTGAAATGCGCAGGCAAATGACGGCACAAAATCCAAAAAAGGAAGTGACTTTCGAAAACTTCAAAAGTGGGTTCTCGTAAAATGAAACCGAAAGCTGTTCAGGTTTAAACCCGGGTGGCGTAGTGCCTGGTTGATGAACACTTTTTACTATCAAAATAACTTCGAAAGCTGCAGGAATTCAAGCTGATCCGGCTGCTAACAAAGCCCGAAGGAAGCTGAGTTGGCTGCTGCCACCGTGAGCAATACTCTAAATACATGACTCT\t*\tRG:Z:a955def6\tbc:B:S,1,1\tbq:i:1\tcx:i:31\tnp:i:1\tqe:i:6183\tqs:i:4151\trq:f:0.88458\tsn:B:f,22.8448,13.8689,14.6461,14.3552\tzm:i:30422 (esc)
m140918_150013_42139_c100697631700000001823144703261565_s1_p0/30422/6234_8214\t4\t*\t0\t255\t*\t*\t0\t0\tAGAGTCATGTATAAGAGTTATTGCTCAGCGGTGGCAGCAGACAACTCAGCTTCCTTTCGGGCCTTTGTTAGCAGCCGGATCCAAGCTTGAATTCCTGCAAGCTCGAGTTATTTGATAGTAAAAGTGTCATCAAACCAGCACTACGGCCGAACCCGGTACCTGAACAGATTCGTTTCATTTTACGAGAAAAACCCACTTTGAAGTTTTGCCGAAAGTCACTTCTTTTTGATTTGTCCGTCATGCTGCGCATTTCACAGAGACTTGAATGTCAGTGTAGTCGTCATCGGGGGGGGGAAGAGCCCTCTACCAGTTTTGCCGTCTACTTCTTTCATGTAAATATCTGGATGTAGGTTTTCTGAACGCAGATATTTGCAGCTTAAAAGTGGATTCGTGTGCCCAGTAGCCCGTTTTCTTCGGGTCCTACGATGTCTTTTGATAACGTCCAGAATTTCAGTACCAGTCAGGTGAATAGAATCGGTATCGCAGTAGATAAATACGATCATAACAAGCCTGCGCTGCCTGTTGATGGTCGTATAGCGTGCCCAGGCCCGTGATAAAGAACCATCGGGGTATATAACAGGGTCTTTCGTTCCTCCTCACCTAGACGAAAAACCCAGAGCACCGTTCTCTTTCAAGGTATGGCCTTTACCGGTAACGTCCGGGTTGGACGCGAATTTAAGCCGTAACAGGCTGTCTCAGCATACAGCTTTCGCCAGCCTGTTTGATGGCCGTCTTCAGAGGTAGTTTTGATATACGTTCCATTTGTCGATAAAGTCCCTTGAGCAGGCCCAGTGGGTTGGCTTTGAACTCAGACGCAGAATATATTCAACATTGTAACAGGTCGTAGTGCTCTTTCATCAGTTCAGATTCAACATTAGACAAGCCACAGGTCAGCATTTCACCGCCGGGAAGAATTTCAAGGTATTCGTTTACCCTTGGTAGAAATGGAACGCTTGTAATCTGGATGGTCGGGATCTAGCCTTTTCAGTTCAAAATTCACACGAATGTGCTGAATGTGCAGAGGGTAATACCTCGTCCCAGACGTATTTACCCTCGAATAAGCGAATCGGCTCGCCGTATCGCAGCAGGCGAGAGTAAACATTTGAGCTGGGTAACAGGGAATTACATCCAAAACCATACCCTTTCGCACGATCTCTTTTTCTTTAAAACGTCATTCAGCCAGGTGAAACCACCAGGTAGGCATAACGAACTTCCTGTCCAGACCCAAGGCTCAGGTCGGGAAAACTTTTTAAACTTCCTTGTGGTGATAATGTCTTTTGAAGCTTTCAGAGAGTCAGAACCTGCGTCATACGATCCAGACCGCTGCTTGAAGCTGGATCAGCAAGCTTCTGCGATAATCTGAATATCGTTTATTAATTAGGCATATTCTTCCGGGTGATTTTGTAACCGACCGGGCGCTCATTATGATAGTCGATGTCGCCCCTTTCAAGTACCGTCAGCTAAAGTCTTTCGCATTTTCTTACCGGAAACGGCAGTTTCTTCAGAGAGTCGTAAGATCACGTGTGGATCTTGCGTTTACCGCTTGTAACCCAGGCAAATATCAATCATATACCACTGGCCATGCGAGAAATGATGGTGTTGTAGGTTATTGGCAGACCATCTGCGGACCATTTTAAAACCGTTACGTTCAGCCAGTTGATGAATGAATGCGCCATGCAAATTTCAGATTGTGGAAGTACAAGGTCAGCCTGACTTTCAGAACCCAAAGCCATAAATTCATCCAGGGAGTTACCATCTTATACTCCGGAGTTGGTCTTCGATGTTCATGTAACCGTATGCCCATACGCGGCAAATCTTCAACCTTGGTGTGTAGTCCTCAAAGTCGCAGGAATACATTTACGTGGCATGTGTTTTCATAATGTATATCTCCTTCTTAAAGTTAAACAAAATTATTTCTAGAGGGGAATTGTTATCCCGCTCACAATCCCCTATCAGTGAGTCGTATTAATTTCGCGGATC\t*\tRG:Z:a955def6\tbc:B:S,1,1\tbq:i:1\tcx:i:31\tnp:i:1\tqe:i:8214\tqs:i:6234\trq:f:0.88458\tsn:B:f,22.8448,13.8689,14.6461,14.3552\tzm:i:30422 (esc)
m140918_150013_42139_c100697631700000001823144703261565_s1_p0/30422/8294_10277\t4\t*\t0\t255\t*\t*\t0\t0\tGATTCCCGCGAAATTAATACGAATCACTATAAGGGGAATTGTGAGCGGATAACAATTCCCCTCTAGAAATAATTTTGTTTAACTTTAAGAGGGACGATATACATATGAACACATGCCTACGTAAAATGTATTCCTGCGAACTGTTGAGACTACCACCAAGGTTGAAGATTTGCCGCGTAATGGGCATACGGTTACATGAACATCGAAGACCACTCCGATATGAAGATTGGTTAACCCCTGGATGAATTTATGGCTTGGGTTCTGAAAGTTCAGGCTGACCTGTACTTCACAATCTGAAATTTGATGGCCGCATTCATCAATCACTGGCTGGAACGTAAAACGGTTTAAAAATGGTCCCGCAGATGGTCTGACAAATTAACTACAACACCATCATTTCTCGCATGGGCCCAGTGGTATATGAAATTGATATTTGCCTGGGTTACAAGGAGGTAAACGCAAGATCCACACGTGGATCTACGACTCTTCTGAAGAAACCTGGCCGTTTCCGTTAAGAAAATGCGAAAGAACTTAAGCTGACGGTAACTGAAAGGCGACATCGACTATCATATAATGAAGCGCCCGTCGTTACAAAATCACCCCGGAAGAATATGCCTTACATTAAAAAACGATATTCAGATTTCGCAGAAGCTCTGCTGATCCAGTTCAAAGCAGGGTCCTGGATCGTAATGACGGCAGGTTCTGACTCTCTGAAAGGCTTCAAAGAACATTATCACCCACCAAGAAGTTTAAAAAGGTTTTCCCGACAACTGAGCCTGGGTCTGGACAAGGAAGTTTCGTTTGCCTACCGTGGTGGTTTTCAACCTGCTGACTGAACCGTTTTAAAAGAAAATAGAGATCGGCGGAAAGGTATGGTTTTTGATGTTAATTCCTGTAACCAGCCTCAAAATGTACTCTCGCCTGCTGCCGTACGGCGGCCGATCGTATTCGAAGGGTAAATACGTCTGGGACCGAGGATAGCCCTCTGCACATTCAGCACATTCGTTGTGAAATTTGAACTGAAGGAAGCTGATCCCGACGCATCCAGATCAAGCGTTCCCATTTTCTACAAGGTAACGAATACCTGAAATCTTCCCGGCGGTGAAATTGCTGCCTGTGGCTGTCTAATGTTGATCTGGAAACTGATGAAAGAGCACTACGAGACCTGTACAATGTTGAATATATCTCTGGTCTGAAGTTCAAAGCAACCACTGGCCTGTTCAAGGACTTTATCGACAAATGGCGTATTATCAAAACTACCTCTGAAGACGCCATCAAACAGCTGGCGAAGCTGATGCTGACAGCCTGTACGGTAAATTCGCGTCGCAACCCGGACGTTTCCGTAAAGTGCCCATACCTGAAAGAGAAACGGTGCTCTGGGTTTTCGTCTAGGTGAGGAGGAAACGAAAGACCCTGTAATATACCCGATGGTGTCTTTTATCACGGCCTGGGCACGCTAGTACGACCAATCACAGCAGCGCAGGCTTGTTATGATCGTATTTCTACTGCGGATACCGATTCTATTCCACCTGACTGGTACTGAAATTCTGGAACGTTATCAAAGACATCGTAGACCCGAAGAAACTGGGCTACTGGGGCACCACGAATCCACTTTTAAGCGTGGCAAAATATCTGACGTCAGAAAACCTACATCCAGGATATTTACATGAAAGAAGTAGACGGCAACTGTAGAGGGCTCTTCCTGACGAACCTACACTGACATCAAGTTCTCTGTGAAATGCGCAGGCATGACGGACCAAAATCAAAAAGGAAGTGAACTTTTCGAAAACTTCAAAGTGGGTTTTCTCGTAAAATGAAACCGAAGCCTGTCAGGTACCGGGTGGCGTAGTGCTGGTTGATCGGACACTTTACTATCAATAACTCGAGCTGCAGAATTCCAAGCTTGGATTCCGGCTGCTAACAAAGCCCGAAAGGAAGCTGAGTTGGCTGCTGCACCGCTGAGCAATAACTCTATACATGACTCAT\t*\tRG:Z:a955def6\tbc:B:S,1,1\tbq:i:1\tcx:i:31\tnp:i:1\tqe:i:10277\tqs:i:8294\trq:f:0.88458\tsn:B:f,22.8448,13.8689,14.6461,14.3552\tzm:i:30422 (esc)
m140918_150013_42139_c100697631700000001823144703261565_s1_p0/30422/10327_12283\t4\t*\t0\t255\t*\t*\t0\t0\tAGAGTCATGTATAGAGTTATTGCTCAGCGGTGGCAGCACCAACTCAGCTTCCTTTCGGCTTTGTTAGCAGCCGATCCAAGCTTGAATTCCTGCAGCTCGGAGTTATTTGATAGTAAAAGTTGTCATCCAAACGCAGCACTACGCCCACCCGTACCTGAACAGGCTTTCGGTTTCATTTTACGAGAAAAACACTTTTGAAAGTTTTCGAAAGTCACTTCCTTTTTTGATTTTGTCCGTCATGCCTGCGCATTTCACAGAGAACTTGATGTCAGTGTAGTCGTCAGGAGAGCCCTCTACCAGTTTGCCGTCTACTTCTTTCATGTAAATATCCTGGAATGTAGGTTTTTCTGACGCAGATTATTTTGCACGCTTAAAAGTGGATTCGTGTGGCCCCAGTAGCCCAGTTTCTTCGGTCTACGATGTCTTTGATACGTCCAGAATTTCAGTAAACAGTCAGGTGAATAGAAATCCGGTATCGCAGTAGAATAATACGATCATAACAACCTGCGCTGCTGTGTGGTCGTATAGCGTGCCCAGGCCGTGATAACAGACACCTCGGGGTAATATACAGGGTCTTTCCGTTCCTCCTCAACCTAGACGAAACCCAGAGCACCGTTCTCTTTTCAGGTATGGCACTTTAACCGGTACGTCCGGGTTGGACGCGAATTTACCGTAGCAGGCTGTTCAGCATCAGCTTTCGCCAGCCTGTTTGATGGCGCTCTTCAGAGGTAGTTTGAATATACGTCCATTTGTCGAATAAAGTCCTTGGAACAGGCCCAGTGGTTGCTTTGAACTTCCAGACCAGAGATATATTTCAACATTGTACAGGTCGTAGTGCTCTTTCCACTCAGTTCCAGATCAACATTAAGACAGCCACAGGTCAGATTTCCCCGCCGGAAGATTCAGGTAATTCTAGTTACCCTTGTAGAAATGGCGACGCTTGATCTGGATGGTCGGGATCCTAGCTTCCCTTCAGTTCAAATTCACAACGAATGTTGCTGAATCTGTGCAGAGGGTAATCCTCGGTCCAGACGTATTTACCCTCGAATACGATGCTCGCCGTACGGCAGCAGCGAGAGTACATTTGAGCTGGTACAGGGAATTAACATCAAAAAACATACTTCGCCGATCTCTTTTTCTTTAAAACGGTCATTCAGCCAGGTGAAACCACCACGGTAGGCATAACGAAACTTCCTGTCCAGACCCAGGCTCAGGTCGGAAAACTTGTTAAACTTCTTGGTGGTGATAATGTCTTTGAAAGCCTTTCAGGAAGTCAGAACCATGCCGTCATCCGATCCAGACCCCTGCTTTGAACTGGAATCAGCAGAGGCTCTGCGATAATCGAATATCGTTTTTAAATGTAGGCATATTTTCTTCGGGGTGATTTGTAACGCGACCGGGCGCTCATTATGATAGTCGATGTCGCCTTTCAGTACCGTCAGCTTAAAGTCTTTCGCAATTTTCTTAACCGACGGCAGTTTCTTCAGAGAGGTCGTAGATCACGGTGTGGATCTTGCGTTTACCCTTGTAACCAGGCAAATATCAATCATATACCACTGGCCCATGCGAGAATGATGGTGTTGTAGGTATTTGGCAGACGCATCTGCGGACCATTTAAACCGTTACGTTCCAGCCAGTTGATGATGAATGCGCCCATCATTTCAGATTTGTGGAAGGTACAGGTCAGCCTGAACTTGTCAGAAACCCAAGCCATAAATTCATCCAGGGAGTACATCTTATAATCTCGAAGTGGTCTTCGATGTTCATGTAACCGTATGCCCATACGCGCAATCTTCACCTTGGTGGTAGTCTGCAGTCGCAGAATAATTTTACGTGGCATGTGTTTCATATGTTATTAGTCTCCTTCTTAAAGTTAAACAAAATTATTTTTAGAAGGGGAATTGTTATCCGCTCACAATTCCCCTATAGTGGAGTCGTATTAATTTCGCGGGTATC\t*\tRG:Z:a955def6\tbc:B:S,1,1\tbq:i:1\tcx:i:31\tnp:i:1\tqe:i:12283\tqs:i:10327\trq:f:0.88458\tsn:B:f,22.8448,13.8689,14.6461,14.3552\tzm:i:30422 (esc)
Invalid-Args:
$ $BAM2SAM --header-only --no-header < $DATADIR/phi29.bam
>|> \d{8} \d{2}:\d{2}:\d{2}\.\d{3} -|- INFO -|- Version -|- [0-9,a-f,x]+|| -|- caught exception: "conflicting arguments requested '--no-header' and '--header-only'" (re)
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