James Bonfield
James Bonfield
I started investigations into how to store such data in SAM. It's non trivial due to BAM's choice of using nibbles to store sequences, thus uppercase bases + ambiguity codes...
The bgzf_read function is long and not something that's likely to get inlined even if it was in the header. However most of the time our calls request a small...
Commit e495718 changed bgzip from unix raw POSIX read() calls to hread(). Unfortunately hread gets its buffer size from stat of the input file descriptor, which can be 4kb for...
Fixes #115. Testing compiler versions is tricky, especially given some vendors wrap up standard compilers as their own, but change version numbers (Apple, Intel) and compilers also often masquerade as...
These are my own work on behalf of GRL. SAM / VCF may take more digging to correctly attribute ownership in order to categorically obtain a license statement, so they...
Hello, I see you are now working on a dev branch of this (affineGap), so please consider this as a feature request. SNAP is astoundingly fast, especially when driven to...
Region filtering permits samtools cat to produce new CRAMs that only cover a specified region. This now acts as a potential replacement for io_lib's [cram_filter](https://github.com/jkbonfield/io_lib/blob/master/progs/cram_filter.c) tool. Eg samtools cat -o...
The AppVeyor builds have become slower to launch and they're also a bit slow on execution. GitHub Actions runs in about half the time. Note this needs https://github.com/samtools/htscodecs/pull/123 merging first,...
- bgzf_getc is slow as it's a heavy function and not inlined. Most of the time though it's just an array fetch, so inline the basic form and revert to...
Even with the same commit hash, sometimes make check works, and sometimes not. For example: https://ci.appveyor.com/project/jkbonfield/bcftools/builds/46710244#L6077 https://ci.appveyor.com/project/samtools/bcftools/builds/46694487#L6077 This test does both bcf and vcf. In both cases the vcf worked,...