James Bonfield
James Bonfield
This fixes #534. We abuse the term Phred-scale, particularly in VCF. This PR also has a minor wording change in SAM to be more explicit. Sometimes VCF uses Phred as...
This also has the CRAM3.0 rANS codec in it. I haven't yet removed this from CRAMv3.tex A prebuilt copy of the document is here: [CRAM_codecs.pdf](https://github.com/samtools/hts-specs/files/3410832/CRAM_codecs.pdf) Code implementing these codecs can...
Cramv4
This adds the CRAMv4.tex document. Note this builds on top of CRAMv3.1, but does so only in as far as CRAMv4 includes all the previous codecs and so the TeX...
It still isn't sufficient to adequately explain how templates with three reads may be encoded. We probably need diagrams for that. However it corrects the issue of being out by...
Some of this is an issue for the data, but some also needs some major clarifications in the spec. - Is contig "" just a typo here: ``` @ seq4-head2[4.3/passed];...
Having been confused by this just now and trying to find out which of 0 and 255 represents a likely event in VCF PL fields, I think we need to...
When we have secondary reads, do we need to have TLEN defined? The recommended practices section under "multiple mappings" states: RNEXT and PNEXT point to the primary line of the...
#### Are you using the latest version of [samtools](https://github.com/samtools/samtools/releases/latest) and [HTSlib](https://github.com/samtools/htslib/releases/latest)? If not, please specify. (run `samtools --version`) Current develop #### Please describe your environment. - OS (run `uname -sr`...
Uses https://github.com/samtools/htslib/pull/1084 By default no change in behaviour, but the -d option now doubles up as a location too. `-d 10` is equiv to `-d 10.0` meaning left end. `-d...
Current policy is now all functions must be static, even in the executable. The only ones left non-static are when used in other .c files or when part of $(LOBJS)...