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Fix issue #803 and add test cases #804

Merged
merged 3 commits into from
Dec 13, 2019
Merged

Fix issue #803 and add test cases #804

merged 3 commits into from
Dec 13, 2019

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38
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@38 38 commented Dec 12, 2019

This was introduced by replacing the header parser with htslib lib standard implementation.

The text header was mistakenly truncated.

Closes #803

@arq5x
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arq5x commented Dec 13, 2019

Thanks Hao!

@arq5x arq5x merged commit 063dd59 into arq5x:master Dec 13, 2019
@mr-c
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mr-c commented Jan 5, 2020

Hello, this fix doesn't work with the samtools 1.10 package in Debian's current development version:

$ echo "@HD     VN:1.5  SO:coordinate" | samtools view -b 
[main_samview] fail to read the header from "-".

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Successfully merging this pull request may close these issues.

Bedtools intersect drops bam header line in latest version
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@38 @arq5x @mr-c