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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
The text was updated successfully, but these errors were encountered:
Fixed #5: output last coverage interval
924e331
In addition to @jkvis fix I added some more changes. We should probably add some tests now that it is used in more places ...
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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
I've created a separate issue for test creation, so we don't necessarily need to stall #4
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When merging is enabled, the last genotype block is never printed. See the attached example file
micro.g.vcf.gz
When merging is disabled, the last block is printed
The text was updated successfully, but these errors were encountered: