The old behavior was that If the bam file name is foo then the index is expected to be at foo.bai.
The new behavior allows file bam file name to be given as foo##idx##bar with the effect that the bam is expected at foo and the index at bar.
This can be particularly useful when the indexes are maintained independently from the bam. For s3 url based bam files this is likely to further eliminate cases where large files need to be copied around, and can instead be left in situ.
This pull request makes Cyrius accept this new notation, while maintaining full backwards compatibility with all old behavior.
xiao-chen-xc
commented
3 years ago
samtools now allows the index file to have a name which is independent of the bam file.
This is documented at several locations, including https://github.com/samtools/samtools/pull/1199 https://github.com/samtools/samtools/pull/1176 https://samtools.github.io/bcftools/bcftools.html
The old behavior was that If the bam file name is
foothen the index is expected to be atfoo.bai. The new behavior allows file bam file name to be given asfoo##idx##barwith the effect that the bam is expected atfooand the index atbar.This can be particularly useful when the indexes are maintained independently from the bam. For s3 url based bam files this is likely to further eliminate cases where large files need to be copied around, and can instead be left in situ.
This pull request makes Cyrius accept this new notation, while maintaining full backwards compatibility with all old behavior.