[KBJ] First round of cleanups #4
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Import is overwritten in the next line with cy_build
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Thanks, standardization looks good. I can't review in depth, but please feel free to merge. |
to allow specifying the `-L .` option for the auditwheel command. Introduced in pypa/cibuildwheel#211 . Fix pysam-developers/pysam#831 .
The Travis job times out after 50'.
This is the version @pm67nz indicates is needed for creating a build from source in pysam-developers/pysam#860 (comment), so I figure we might as well enforce it everywhere?
…ader added with it have double-quoting rules in accordance to rules specified in VCF4.2 and VCF4.3 specifications
Force arg to bytes to support non-ASCII encoding
Removal of unused import
Fix wheel building on TravisCI
Prevent segfault on Python 2.7 AlignedSegment.compare(other=None)
Bump minimum Cython version
Restore twine upload on tag
(issue #881) Fix add_meta function in libcbcf.pyx, so meta-information lines in he…
The legacy import command was broken in Samtools 1.10 (hat tip @mr-c) and has been removed from future Samtools (see samtools/samtools#1185). Use the equivalent `samtools view` command instead. Update 00README.txt to the current text in samtools/examples/00README.txt that it was copied from, and delete the samtools command samples as they are not relevant for pysam.
Several ancient test cases fail with samtools 1.10, as its improved header facilities require greater baseline validity from input data: Remove TestDeNovoConstructionUserTags and example_user_header.sam. These were added in 748ccc8 due to https://code.google.com/archive/p/pysam/issues/96 but this was misguided: only `@HD/@SQ/@RG/@PG/@CO` have ever been valid in SAM. Replace tabs with spaces in rg_with_tab.sam. Samtools now parses and requires that all tabs do actually delimit header fields, so pysam's CL-to-end-of-line extension is no longer testable. Fix whitespace editing error in example_empty_with_header.sam header.
Work around the behaviour change in Samtools 1.10 whereby commands that output SAM/BAM/CRAM now default to adding their own `@PG` headers. Use GNU Make functions to probe the usage display for the existence of a --no-PG option, to work with either <= 1.9 or >= 1.10.
When converting to CRAM, Samtools 1.10 now preserves incorrect NM values in its input data, whereas previous versions would effectively correct them. Change the NM values in ex3.sam to be correct to avoid this difference between samtools versions, and adjust the SAM/BAM test cases accordingly.
Add a Python 3.8 build to the Travis build matrix.
Silence wget. No longer need to force use of $PREFIX/{include,lib};
instead ensure we don't see the HTSlib headers in the Conda environment
ahead of pysam's included copy of HTSlib.
Display a more meaningful selection of the HTSlib configuration variables.
Fix typos in the FAQ
Pysam still bundles htslib/etc 1.9, but with these changes all tests pass when used together with external samtools/bcftools/etc provided by either samtools/etc 1.9 or samtools/etc 1.10.x.
Pysam's build and tests do not use {htslib,samtools,bcftools}/test
so remove them from the repository and do not import them in future.
Similarly samtools/misc and bcftools/plugins are unused, so remove
them from the import list entirely (rather than listing most misc/*
files and having a note to remove plugins/* manually).
Update so that import.py can be used for htslib too: add the build
infrastructure, but don't run _update_pysam_files() for htslib.
Don't list hfile_irods.c, which was moved to its own repository long
ago and removed from HTSlib 1.4.
Re-import htslib, bcftools, and samtools with the updated script to remove unused subdirectories and sundries, notably */test. (Previously the bulk of */test etc were omitted, but various items had crept back in as this was not fully automated.) Preserve the hand-made */version.h files and samtools/bamtk.c.pysam.c fix and the backported htslib/configure fix.
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