Move regidx code to htslib #865
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jmarshall
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Mar 2, 2022
Exclude samtools/bam2bcf.[ch] which (starting in samtools 1.15) are only used by bam_tview.c (which we already exclude) and contain functions that collide with bcftools. Remove obsolete exclusions for removed items. In import/pysam.h, add prefixes to several more functions that otherwise conflict between libcsamtools and libcbcftools. Fixes pysam-developers#1081. In bcftools/regidx.h, add prefixes to all functions, as these conflict with those provided by htslib/htslib/regidx.h. This is done locally within bcftools (rather than via import/pysam.h) as this issue may be resolved in future bcftools imports by PR samtools/bcftools#865.
jmarshall
added a commit
to jmarshall/pysam
that referenced
this pull request
Mar 2, 2022
Exclude samtools/bam2bcf.[ch] which (starting in samtools 1.15) are only used by bam_tview.c (which we already exclude) and contain functions that collide with bcftools. Remove obsolete exclusions for removed items. In import/pysam.h, add prefixes to several more functions that otherwise conflict between libcsamtools and libcbcftools. Fixes pysam-developers#1081. In bcftools/regidx.h, add prefixes to all functions, as these conflict with those provided by htslib/htslib/regidx.h. This is done locally within bcftools (rather than via import/pysam.h) as this issue may be resolved in future bcftools imports by PR samtools/bcftools#865.
jmarshall
added a commit
to jmarshall/pysam
that referenced
this pull request
Mar 3, 2022
Exclude samtools/bam2bcf.[ch] which (starting in samtools 1.15) are only used by bam_tview.c (which we already exclude) and contain functions that collide with bcftools. Remove obsolete exclusions for removed items. In import/pysam.h, add prefixes to several more functions that otherwise conflict between libcsamtools and libcbcftools. Fixes pysam-developers#1081. In bcftools/regidx.h, add prefixes to all functions, as these conflict with those provided by htslib/htslib/regidx.h. This is done locally within bcftools (rather than via import/pysam.h) as this issue may be resolved in future bcftools imports by PR samtools/bcftools#865.
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