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Last genotype block not printed when merging is enabled (on min_dp branch) #5

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Redmar-van-den-Berg opened this issue Jul 22, 2020 · 3 comments

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@Redmar-van-den-Berg
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When merging is enabled, the last genotype block is never printed. See the attached example file
micro.g.vcf.gz

./gvcf2coverage -t 120 < micro.g.vcf 
chrM	0	152	2
chrM	750	1438	2
.
.
.
chrM	16022	16023	2

When merging is disabled, the last block is printed

./gvcf2coverage -t 120 -n < micro.g.vcf
chrM	0	151	2
chrM	151	152	2
chrM	750	1437	2
.
.
.
chrM	16022	16023	2
chrM	16559	16569	2
jkvis added a commit that referenced this issue Jul 22, 2020
@marksantcroos
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In addition to @jkvis fix I added some more changes.
We should probably add some tests now that it is used in more places ...

@Redmar-van-den-Berg
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When I added gvcf2coverage to the Hutspot pipeline I also added some tests based on a g.vcf file for the mitochondrion. They are pretty high level (since they only test the output file), but it's a start:
https://git.lumc.nl/klinische-genetica/capture-lumc/hutspot/-/blob/devel/tests/test_integration_run.yml#L254

@marksantcroos
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I've created a separate issue for test creation, so we don't necessarily need to stall #4

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