Adapt test results to latest samtools

Last-Update: Fri, 13 Dec 2019 21:50:03 +0100

Gbp-Pq: Name results_with_latest_samtools.patch

diff --git a/tests/src/cram/pbbamify.t.in b/tests/src/cram/pbbamify.t.in
index c68ba432278579ea5b0284c4ddad9d3e52f282d8..d725a245f15c051b70722f656e8b5aec9e9eba40 100644 (file)
--- a/tests/src/cram/pbbamify.t.in
+++ b/tests/src/cram/pbbamify.t.in
@@ -8,7 +8,7 @@ Setup:
 
 Forward alignments with and without user specified tags, one alignment with undefined mapq, some alignments with basic CIGAR operations, 2 alignemtns with hard clipping, and several invalid alignments (1 without a seq field and 1 not present in the dataset) which should be skipped:
 
-  $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-1.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | $SAMTOOLS view -h
+  $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-1.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | $SAMTOOLS view -h | grep -v 'CL:samtools view -h'
   @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc)
   @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)
   @RG\tID:8d2370c0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_1\tPM:SEQUEL (esc)
@@ -36,7 +36,7 @@ Forward alignments with and without user specified tags, one alignment with unde
   $ rm pbbamify.log
 
 Reverse alignments: 2 primary alignments and 7 secondary, 6 alignments with extended CIGAR and 2 with basic CIGAR strings, 1 alignment with undefined (255) mapq, 2 alignments with hard clipping, 1 alignment with user defined tag. All alignments have a read group assigned which is different than the dataset.
-  $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-2.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_2.subreads.bam | $SAMTOOLS view -h
+  $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-2.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_2.subreads.bam | $SAMTOOLS view -h | grep -v 'CL:samtools view -h'
   @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc)
   @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)
   @RG\tID:7a515ee0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_2\tPM:SEQUEL (esc)
@@ -60,7 +60,7 @@ Reverse alignments: 2 primary alignments and 7 secondary, 6 alignments with exte
 
 CCS read:
 
-  $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-3.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_3.subreads.bam | $SAMTOOLS view -h
+  $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-3.bam $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_3.subreads.bam | $SAMTOOLS view -h | grep -v 'CL:samtools view -h'
   @HD\tVN:1.5\tSO:unknown\tpb:3.0.1 (esc)
   @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)
   @RG\tID:67e06f58\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=100-862-200;SEQUENCINGKIT=101-093-700;BASECALLERVERSION=5.0.0.5049;FRAMERATEHZ=80.000000\tPU:synthetic_movie_3\tPM:SEQUEL (esc)
@@ -74,7 +74,7 @@ CCS read:
 
 No verbose output:
 
-  $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-1.bam --verbose-level=0 $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | $SAMTOOLS view -h
+  $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-1.bam --verbose-level=0 $DATADIR/pbbamify/synthetic-ref-1.fa $DATADIR/pbbamify/synthetic_movie_1.subreads.bam | $SAMTOOLS view -h | grep -v 'CL:samtools view -h'
   @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc)
   @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)
   @RG\tID:8d2370c0\tPL:PACBIO\tDS:READTYPE=SUBREAD;Ipd:CodecV1=ip;PulseWidth:CodecV1=pw;BINDINGKIT=100-862-200;SEQUENCINGKIT=100-861-800;BASECALLERVERSION=5.0.0.5552;FRAMERATEHZ=80.000000\tPU:synthetic_movie_1\tPM:SEQUEL (esc)
@@ -101,7 +101,7 @@ No verbose output:
 
 Test on a dataset, input contains alignments from all subread sets.
 
-  $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-all.bam $DATADIR/pbbamify/synthetic-ref-1.fa $GENERATEDDATADIR/synthetic_movie_all.subreadset.xml | $SAMTOOLS view -h
+  $ $PBBAMIFY --log-file=pbbamify.log --input=$DATADIR/pbbamify/input-aligned-all.bam $DATADIR/pbbamify/synthetic-ref-1.fa $GENERATEDDATADIR/synthetic_movie_all.subreadset.xml | $SAMTOOLS view -h | grep -v 'CL:samtools view -h'
   @HD\tVN:1.5\tSO:unknown\tpb:3.0.3 (esc)
   @SQ\tSN:synthetic_ref_1\tLN:150\tM5:e1e940d621d949c9617566ddf3055922 (esc)
   @RG\tID:67e06f58\tPL:PACBIO\tDS:READTYPE=CCS;BINDINGKIT=100-862-200;SEQUENCINGKIT=101-093-700;BASECALLERVERSION=5.0.0.5049;FRAMERATEHZ=80.000000\tPU:synthetic_movie_3\tPM:SEQUEL (esc)

diff --git a/tests/src/cram/pbmerge_aligned_ordering.t.in b/tests/src/cram/pbmerge_aligned_ordering.t.in
index 58171bbfe91e201a08619bda81bfb12cf275ef30..106069248e76b557c6f1bf67604d91b2b389b434 100644 (file)
--- 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 PBI):
 
   $ $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 PBI):
 
   $ $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)

diff --git a/tests/src/cram/pbmerge_dataset.t.in b/tests/src/cram/pbmerge_dataset.t.in
index 1c7cb7a96d153a9ff5ded4a4f7ce3c6c3a5ca15a..e26f2ccc3ebc680d4c6838cf16010b094db5df2d 100644 (file)
--- 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)

diff --git a/tests/src/cram/pbmerge_fofn.t.in b/tests/src/cram/pbmerge_fofn.t.in
index 34e9af65db8b388f567c663a42e400319fc5a2e0..5c776bd5769017dbe9ee20ae9ab92cd4dbe88e1c 100644 (file)
--- 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)

diff --git a/tests/src/cram/pbmerge_mixed_ordering.t.in b/tests/src/cram/pbmerge_mixed_ordering.t.in
index f558defc529a8e34c3f7a0b5720e0404ef02c39f..5fe6ba2c11206723eff1bdccbf8121e66aff1f52 100644 (file)
--- 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)

diff --git a/tests/src/cram/pbmerge_pacbio_ordering.t.in b/tests/src/cram/pbmerge_pacbio_ordering.t.in
index f52759ffd16974118689519572e83e7e27e64970..3b96715c31ce9737a1462a4b46f9d4bec3e583c3 100644 (file)
--- 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 PBI):
 
   $ $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 PBI):
 
   $ $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)