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|
Description: Adapt test results to latest samtools
Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 13 Dec 2019 21:50:03 +0100
--- a/tests/src/cram/pbmerge_pacbio_ordering.t.in
+++ b/tests/src/cram/pbmerge_pacbio_ordering.t.in
@@ -13,7 +13,7 @@ Setup:
Sanity Check:
- $ $BAM2SAM --header-only $HQREGION_BAM
+ $ $BAM2SAM --header-only $HQREGION_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie (esc)
@PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc)
@@ -23,7 +23,7 @@ Sanity Check:
$ $BAM2SAM --no-header $HQREGION_BAM | cut -f 1
ArminsFakeMovie/100000/2659_7034
- $ $BAM2SAM --header-only $SCRAPS_BAM
+ $ $BAM2SAM --header-only $SCRAPS_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie (esc)
@PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc)
@@ -105,7 +105,7 @@ Normal Merge:
$ $PBMERGE $HQREGION_BAM $SCRAPS_BAM > $MERGED_BAM
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@@ -192,7 +192,7 @@ Shuffle Input:
$ $PBMERGE $SCRAPS_BAM $HQREGION_BAM > $MERGED_BAM
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@@ -279,7 +279,7 @@ Explicit Output Filename (also enables P
$ $PBMERGE -o $MERGED_BAM $HQREGION_BAM $SCRAPS_BAM
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@@ -370,7 +370,7 @@ Explicit Output Filename (with disabled
$ $PBMERGE -o $MERGED_BAM --no-pbi $HQREGION_BAM $SCRAPS_BAM
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
--- a/tests/src/cram/pbmerge_mixed_ordering.t.in
+++ b/tests/src/cram/pbmerge_mixed_ordering.t.in
@@ -12,7 +12,7 @@ Setup:
Sanity Check:
- $ $BAM2SAM --header-only $UNALIGNED_BAM
+ $ $BAM2SAM --header-only $UNALIGNED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:ca75d884\tPL:PACBIO\tDS:READTYPE=HQREGION;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:Frames=ip;PulseWidth:Frames=pw;PkMid=pm;PkMean=pa;LabelQV=pq;AltLabel=pt;AltLabelQV=pv;PulseMergeQV=pg;PulseCall=pc;PrePulseFrames=pd;PulseCallWidth=px;BINDINGKIT=100372700;SEQUENCINGKIT=100356200;BASECALLERVERSION=0.1;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie (esc)
@PG\tID:baz2bam-0.15.0\tPN:baz2bam\tVN:0.15.0 (esc)
@@ -22,7 +22,7 @@ Sanity Check:
$ $BAM2SAM --no-header $UNALIGNED_BAM | cut -f 1
ArminsFakeMovie/100000/2659_7034
- $ $BAM2SAM --header-only $ALIGNED_BAM
+ $ $BAM2SAM --header-only $ALIGNED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@RG\tID:a9a22406c5\tDS:READTYPE=SUBREAD;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTag=dt\tPL:PACBIO\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377 (esc)
--- a/tests/src/cram/pbmerge_aligned_ordering.t.in
+++ b/tests/src/cram/pbmerge_aligned_ordering.t.in
@@ -13,7 +13,7 @@ Setup:
Sanity Check:
- $ $BAM2SAM --header-only $INPUT_1
+ $ $BAM2SAM --header-only $INPUT_1 | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@RG\tID:a9a22406c5\tDS:READTYPE=SUBREAD;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTag=dt\tPL:PACBIO\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377 (esc)
@@ -31,7 +31,7 @@ Sanity Check:
m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc)
m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc)
- $ $BAM2SAM --header-only $INPUT_2
+ $ $BAM2SAM --header-only $INPUT_2 | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@RG\tID:a9a22406c5\tDS:READTYPE=SUBREAD;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTag=dt\tPL:PACBIO\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377 (esc)
@@ -53,7 +53,7 @@ Normal Merge:
$ $PBMERGE $INPUT_1 $INPUT_2 > $MERGED_BAM
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
@@ -88,7 +88,7 @@ Shuffle Input:
$ $PBMERGE $INPUT_2 $INPUT_2 > $MERGED_BAM
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
@@ -123,7 +123,7 @@ Explicit Output Filename (also enables P
$ $PBMERGE -o $MERGED_BAM $INPUT_1 $INPUT_2
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
@@ -162,7 +162,7 @@ Explicit Output Filename (with disabled
$ $PBMERGE -o $MERGED_BAM --no-pbi $INPUT_1 $INPUT_2
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
--- a/tests/src/cram/pbmerge_fofn.t.in
+++ b/tests/src/cram/pbmerge_fofn.t.in
@@ -14,7 +14,7 @@ Setup:
Sanity Check:
- $ $BAM2SAM --header-only $INPUT_1
+ $ $BAM2SAM --header-only $INPUT_1 | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@RG\tID:0d7b28fa\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=100-619-300;SEQUENCINGKIT=100-619-400;BASECALLERVERSION=3.0;FRAMERATEHZ=100\tPU:singleInsertion\tPM:SEQUEL (esc)
@@ -26,7 +26,7 @@ Sanity Check:
singleInsertion/100/0_111\tlambda_NEB3011\t9378 (esc)
singleInsertion/100/0_111\tlambda_NEB3011\t9378 (esc)
- $ $BAM2SAM --header-only $INPUT_2
+ $ $BAM2SAM --header-only $INPUT_2 | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@RG\tID:b89a4406\tDS:READTYPE=SUBREAD;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;FRAMERATEHZ=100;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;SubstitutionTag=st;DeletionTag=dt\tPL:PACBIO\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
@@ -54,7 +54,7 @@ Normal Merge from FOFN:
$ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
Found
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@RG\tID:0d7b28fa\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=100-619-300;SEQUENCINGKIT=100-619-400;BASECALLERVERSION=3.0;FRAMERATEHZ=100\tPU:singleInsertion\tPM:SEQUEL (esc)
@@ -92,7 +92,7 @@ Normal Merge from FOFN (disabled PBI):
$ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
Not found
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.3 (esc)
@SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
@RG\tID:0d7b28fa\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=100-619-300;SEQUENCINGKIT=100-619-400;BASECALLERVERSION=3.0;FRAMERATEHZ=100\tPU:singleInsertion\tPM:SEQUEL (esc)
--- a/tests/src/cram/pbmerge_dataset.t.in
+++ b/tests/src/cram/pbmerge_dataset.t.in
@@ -59,7 +59,7 @@ Normal Merge from XML:
$ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
Found
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@@ -91,7 +91,7 @@ Normal Merge from XML (disabled PBI):
$ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
Not found
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@@ -122,7 +122,7 @@ Write to stdout:
$ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
Not found
- $ $BAM2SAM --header-only $MERGED_BAM
+ $ $BAM2SAM --header-only $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.1\tSO:unknown\tpb:3.0.1 (esc)
@RG\tID:8aaede36\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
@RG\tID:e83fc9c6\tPL:PACBIO\tDS:READTYPE=SCRAP;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;Ipd:CodecV1=ip;BINDINGKIT=FakeBindKit;SEQUENCINGKIT=FakeSeqKit;BASECALLERVERSION=0.2.0;FRAMERATEHZ=100.000000\tPU:ArminsFakeMovie\tPM:SEQUEL (esc)
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