[Feature request] Parsing gzipped file for --barcode-whitelist and --barcode-translation

[bli25]

trafficstars

For 10x data, cellranger-atac/cellranger-arc make their whitelist in .tsv.gz format. It would be convenient if chromap can take gzipped file as input here (similar to fastq file).

Thanks for developing such a useful tool!

[mourisl]

For these files that only need to scan once, would command like ./chromap ... --barcode-whitelist <(zcat whitelist.tsv.gz) work on your platform?

[bli25]

Hi @mourisl , yes, it works. However, we are building workflows, which means we do not have control of what white list people will provide (either gzipped or not). We can take care of it at the workflow level (i.e. test if suffix is 'gz' and if so, gunzip). But I think it is more elegant if chromap can take care of this step because for FASTQ files, you already have support for both .fq and .fq.gz.

[mourisl]

Sorry for the delayed replay after almost one year, which I totally forgot to work on until another recent issue. We just added the feature to directly support gzipped whitelist file #127 . If your team is still interested in this feature, could you please give it a try?