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MergeBamAlignment UNMAP_CONTAMINANT_READS does not set the CIGAR to "*" #1134

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jleinenbach opened this issue Mar 9, 2018 · 0 comments · Fixed by #1316
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MergeBamAlignment UNMAP_CONTAMINANT_READS does not set the CIGAR to "*" #1134

jleinenbach opened this issue Mar 9, 2018 · 0 comments · Fixed by #1316

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@jleinenbach
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jleinenbach commented Mar 9, 2018 •
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Bug Report

Affected tool(s)

MergeBamAlignment with option UNMAP_CONTAMINANT_READS=true

Affected version(s)

  • Tested with 2.17.10-6

Description

SAM files processed with MergeBamAlignment with UNMAP_CONTAMINANT_READS=true create the following error message when processed with other Picard tools:

Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing text SAM file. CIGAR must be '*' if RNAME is not specified;

Steps to reproduce

Process a SAM file with MergeBamAlignment and UNMAP_CONTAMINANT_READS=true option, then verify it with ValidateSamFile.

Expected behavior

CIGAR should be set to '*' for unmapped reads.

Actual behavior

CIGAR was not changed when unmapping contaminant reads:
Line: XXXX 93 * 0 0 150M * 0 0 GACAGCCACGTTCTGCAAACCTCCTTTTGGGCAGTGTGATTCCTTTTAGCCCTCAGAATGGTTTCTAC
TACAGATATATAGGCAGACAGCAAGATCTCAGAGAGCAAGCAGGCTGTGAGATCCTTCCAGCCAGCAAGGGGCTATTGATCC JJJJFJJJJJJJJJFJJJJJJFJFAFFJJJAJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJFJJFJJJJJJJJJJJJJJJJJF
-JJJJJJJJJJJJJJFFJJJAJJJAJFJJJJFJAFJFAFJJAFJAFAAAA RG:Z:XXX_L5 CO:Z:Cross-species contamination AS:i:150 XS:i:19
yfarjoun pushed a commit that referenced this issue Apr 16, 2019
- fixes #1134
0dfe702
@yfarjoun yfarjoun mentioned this issue Apr 16, 2019
Merged
yfarjoun pushed a commit that referenced this issue Jul 16, 2019
Fixes several small issues that needed some help (#1316)
da28cb4 
* This PR addresses a hodgepodge of issues in github, and also (while I was at it) adds some tests and a few stratifiers to CollectSamErrorMetrics.
- test for MergeBamAlignment
- fixes #1134
- refactored a bam reading loop in a test
- added unmapping strategy that makes the result "invalid" (for folks who do not wish to change the mapping quality or cigar even if it means creating an invalid record)
- fixed a test
- fix documentation in FilterSamReads (fixes #1322)
mjhipp pushed a commit to mjhipp/picard that referenced this issue Aug 1, 2019
@mjhipp
Fixes several small issues that needed some help (broadinstitute#1316)
e08e21e 
* This PR addresses a hodgepodge of issues in github, and also (while I was at it) adds some tests and a few stratifiers to CollectSamErrorMetrics.
- test for MergeBamAlignment
- fixes broadinstitute#1134
- refactored a bam reading loop in a test
- added unmapping strategy that makes the result "invalid" (for folks who do not wish to change the mapping quality or cigar even if it means creating an invalid record)
- fixed a test
- fix documentation in FilterSamReads (fixes broadinstitute#1322)
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Fixes several small issues that needed some help broadinstitute/picard
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@jleinenbach