wip/py-pysam: use pkgsrc htslib

[Brook Milligan <brook%nmsu.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Fri Jun 4 20:40:33 2021 -0600
Changeset:	beddc34a42a47b33a13424fbefdae5cebadbbc70

Modified Files:
	py-pysam/Makefile
	py-pysam/PLIST

Log Message:
wip/py-pysam: use pkgsrc htslib

Although py-pysam includes its own copy of htslib, it seems preferable
to use the pkgsrc version.  Most of this was already implemented; i.e.,
HTSLIB_INCLUDE_DIR AND HTSLIB_LIBRARY_DIR were defined in the make
environment.  However, HTSLIB_MODE was missing.  This adds that and
removes the htslib files from PLIST.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=beddc34a42a47b33a13424fbefdae5cebadbbc70

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 py-pysam/Makefile |  1 +
 py-pysam/PLIST    | 33 ---------------------------------
 2 files changed, 1 insertion(+), 33 deletions(-)

diffs:
diff --git a/py-pysam/Makefile b/py-pysam/Makefile
index b5efb6bbbf..d62b3fb6ee 100644
--- a/py-pysam/Makefile
+++ b/py-pysam/Makefile
@@ -12,6 +12,7 @@ LICENSE=	mit
 
 USE_TOOLS+=	gmake
 
+MAKE_ENV+=	HTSLIB_MODE=external
 MAKE_ENV+=	HTSLIB_INCLUDE_DIR=${BUILDLINK_PREFIX.htslib}/include
 MAKE_ENV+=	HTSLIB_LIBRARY_DIR=${BUILDLINK_PREFIX.htslib}/lib
 
diff --git a/py-pysam/PLIST b/py-pysam/PLIST
index e0aa924cb7..74e5521735 100644
--- a/py-pysam/PLIST
+++ b/py-pysam/PLIST
@@ -47,39 +47,6 @@ ${PYSITELIB}/pysam/include/bcftools/tsv2vcf.h
 ${PYSITELIB}/pysam/include/bcftools/vcfbuf.h
 ${PYSITELIB}/pysam/include/bcftools/vcmp.h
 ${PYSITELIB}/pysam/include/bcftools/version.h
-${PYSITELIB}/pysam/include/htslib/bcf_sr_sort.h
-${PYSITELIB}/pysam/include/htslib/config.h
-${PYSITELIB}/pysam/include/htslib/hfile_internal.h
-${PYSITELIB}/pysam/include/htslib/hts_internal.h
-${PYSITELIB}/pysam/include/htslib/htslib/bgzf.h
-${PYSITELIB}/pysam/include/htslib/htslib/cram.h
-${PYSITELIB}/pysam/include/htslib/htslib/faidx.h
-${PYSITELIB}/pysam/include/htslib/htslib/hfile.h
-${PYSITELIB}/pysam/include/htslib/htslib/hts.h
-${PYSITELIB}/pysam/include/htslib/htslib/hts_defs.h
-${PYSITELIB}/pysam/include/htslib/htslib/hts_endian.h
-${PYSITELIB}/pysam/include/htslib/htslib/hts_log.h
-${PYSITELIB}/pysam/include/htslib/htslib/hts_os.h
-${PYSITELIB}/pysam/include/htslib/htslib/kbitset.h
-${PYSITELIB}/pysam/include/htslib/htslib/kfunc.h
-${PYSITELIB}/pysam/include/htslib/htslib/khash.h
-${PYSITELIB}/pysam/include/htslib/htslib/khash_str2int.h
-${PYSITELIB}/pysam/include/htslib/htslib/klist.h
-${PYSITELIB}/pysam/include/htslib/htslib/knetfile.h
-${PYSITELIB}/pysam/include/htslib/htslib/kseq.h
-${PYSITELIB}/pysam/include/htslib/htslib/ksort.h
-${PYSITELIB}/pysam/include/htslib/htslib/kstring.h
-${PYSITELIB}/pysam/include/htslib/htslib/regidx.h
-${PYSITELIB}/pysam/include/htslib/htslib/sam.h
-${PYSITELIB}/pysam/include/htslib/htslib/synced_bcf_reader.h
-${PYSITELIB}/pysam/include/htslib/htslib/tbx.h
-${PYSITELIB}/pysam/include/htslib/htslib/thread_pool.h
-${PYSITELIB}/pysam/include/htslib/htslib/vcf.h
-${PYSITELIB}/pysam/include/htslib/htslib/vcf_sweep.h
-${PYSITELIB}/pysam/include/htslib/htslib/vcfutils.h
-${PYSITELIB}/pysam/include/htslib/textutils_internal.h
-${PYSITELIB}/pysam/include/htslib/thread_pool_internal.h
-${PYSITELIB}/pysam/include/htslib/version.h
 ${PYSITELIB}/pysam/include/samtools/bam.h
 ${PYSITELIB}/pysam/include/samtools/bam2bcf.h
 ${PYSITELIB}/pysam/include/samtools/bam_endian.h