In samtools/samtools#1884 we saw a BAM file downloaded via a web browser and ungzipped. htsfile reported this file as follows:
$ htsfile wgEncode-browser.bam
wgEncode-browser.bam: BAM version 1 sequence data
In isolation it's not obvious that this is reporting that the BAM file is not BGZF-compressed as normal. (For usual BAM files, htsfile reports BAM version 1 compressed sequence data, but if you don't have one handy to compare…)
This PR adds “uncompressed” for uncompressed files in formats, like BAM and BCF, that are normally compressed, to make this clear. Thus:
$ htsfile wg*.bam
wgEncode-browser.bam: BAM version 1 uncompressed sequence data
wgEncode-curl.bam: BAM version 1 compressed sequence data
In samtools/samtools#1884 we saw a BAM file downloaded via a web browser and ungzipped.
htsfilereported this file as follows:In isolation it's not obvious that this is reporting that the BAM file is not BGZF-compressed as normal. (For usual BAM files,
htsfilereportsBAM version 1 compressed sequence data, but if you don't have one handy to compare…)This PR adds “uncompressed” for uncompressed files in formats, like BAM and BCF, that are normally compressed, to make this clear. Thus: