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

varda / varda2_preprocessing

Extract coverage information from gVCF and variants from VCF files and output in tabular format.

MIT License

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

Open Redmar-van-den-Berg opened 4 years ago

Redmar-van-den-Berg commented 4 years ago

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

marksantcroos commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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