Update imports to htslib/samtools/bcftools 1.11#962
Merged
jmarshall merged 5 commits intopysam-developers:masterfrom Jan 12, 2021
Merged
Update imports to htslib/samtools/bcftools 1.11#962jmarshall merged 5 commits intopysam-developers:masterfrom
jmarshall merged 5 commits intopysam-developers:masterfrom
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Avoid exercising samtools/htslib#1142 (present in the HTSlib-1.11 release), which leads to test failures due to the way we test using iterators. This is not what these pysam test cases are trying to test, so alter the input data file to avoid the issue.
For each package:
rm -rf htslib; python3 devtools/import.py htslib .../htslib-1.11
rm -rf samtools; python3 devtools/import.py samtools .../samtools-1.11
rm -rf bcftools; python3 devtools/import.py bcftools .../bcftools-1.11
(Don't bother adding {sam,bcf}tools/htslib-1.11/{LICENSE,README}.)
Add new ampliconclip and ampliconstats commands to pysam/samtools.py.
Apply PR samtools/htslib#1150. The hfile irods plugin depends on a constructed symbol name which was no longer being used.
This was referenced Oct 20, 2020
Apply PR samtools/htslib#1184. On macOS, plugins pulling in libhts.dylib conflicts with a statically linked libhts.a from the main executable.
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Season's greetings to all… @AndreasHeger @kevinjacobs-progenity @bioinformed — does anyone want to review this, or shall I just merge it? The update to 1.11 was straightforward (e.g., compared to the 1.10 one). |
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Apologies for the delay. This looks sensible and uncontroversial. My quick tests passed. |
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Import htslib, samtools, and bcftools 1.11:
First alter tests/pysam_data/ex1.sam.gz (and files built from it) to avoid exercising a htslib-1.11 bug as described in Adds linear index support samtools/htslib#1031 (comment); here we are testing the pysam bindings not this particular behaviour, so simply avoiding the problem is legitimate.
(You will need to regenerate these files with
git clean -xf tests/pysam_data; make -C tests/pysam_dataor similar before running the pysam tests with htslib-1.11.)Import the 1.11 releases, and add the new
ampliconclipandampliconstatssubcommands to pysam/samtools.py.Backport Variable name used by dlsym in load_plugin corrected. samtools/htslib#1150 and Don't link plugins with libhts.dylib on macOS (correction to PR 1072) samtools/htslib#1184 to avoid potential plugin problems.
Bump version numbers in documentation.