jmarshall

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John Marshall jmarshall

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Wānaka, New Zealand
13:24 (UTC +13:00)
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Pinned

samtools/htslib Public

C library for high-throughput sequencing data formats

C 679 426
pysam-developers/pysam Public

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

C 641 250
samtools/hts-specs Public

Specifications of SAM/BAM and related high-throughput sequencing file formats

TeX 555 172
cansam Public

C++ binding for SAM/BAM files

C++ 6 1

218 contributions in the last year

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Activity overview

Contributed to pysam-developers/pysam, samtools/htslib, samtools/samtools and 26 other repositories

Contribution activity

March 2023

Created 5 commits in 1 repository

pysam-developers/pysam 5 commits

Created a pull request in pysam-developers/pysam that received 2 comments

Fix building htscodecs SIMD code on multi-arch macOS

On macOS, hack the htslib (really just htscodecs) build a little bit so that the htscodecs SIMD code is only built for one architecture, i.e., eith…

+69 −2 • 2 comments

Opened 1 other pull request in 1 repository

pysam-developers/pysam 1 merged

Update imports to htslib/samtools/bcftools 1.17 Mar 10

Reviewed 1 pull request in 1 repository

samtools/samtools 1 pull request

Expand the mpileup man page default filtering. Mar 7

Created an issue in samtools/htscodecs that received 9 comments

SIMD code selection and configury is incorrect for multi-arch compilation

[This investigation has occurred in a pysam context, which uses htslib's bundled-htscodecs build system rather than htscodecs's native build system…

9 comments