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PrintReadsHeader: a new tool to print a BAM/SAM/CRAM header to a file #6153

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merged 4 commits into from
Oct 24, 2019
Merged

PrintReadsHeader: a new tool to print a BAM/SAM/CRAM header to a file #6153

merged 4 commits into from
Oct 24, 2019

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droazen
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@droazen droazen commented Sep 10, 2019

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droazen commented Sep 10, 2019

@michaelgatzen Please review

@droazen droazen changed the title PrintHeader: a new tool to print a BAM header to a file PrintBAMHeader: a new tool to print a BAM header to a file Sep 10, 2019
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droazen commented Sep 10, 2019

Example usage:

/gatk PrintBAMHeader -I gs://hellbender/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam -O header_for_michael.txt

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michaelgatzen approved these changes Sep 16, 2019
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I added an integration test which just checks one tiny BAM header. I couldn't think of too many "edge cases" there, feel free to let me know if I should implement some more tests!

@droazen droazen changed the title PrintBAMHeader: a new tool to print a BAM header to a file PrintReadsHeader: a new tool to print a BAM/SAM/CRAM header to a file Oct 24, 2019
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droazen commented Oct 24, 2019

Renamed the tool to PrintReadsHeader, and did some minor cleanup in preparation for merge.

@droazen droazen assigned droazen and unassigned michaelgatzen Oct 24, 2019
@droazen droazen merged commit 34cdadf into master Oct 24, 2019
@droazen droazen deleted the dr_printheader branch October 24, 2019 20:05
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