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py-pysam: Work toward update to 0.16.0

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Jul 27 19:33:26 2023 -0500
Changeset:	c5b9f5d496db3a35f5fabbb6e4977abb90af89df

Modified Files:
	py-pysam/Makefile
	py-pysam/PLIST
	py-pysam/distinfo
	py-pysam/patches/patch-setup.py
Removed Files:
	py-pysam/patches/patch-cy__build.py

Log Message:
py-pysam: Work toward update to 0.16.0

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c5b9f5d496db3a35f5fabbb6e4977abb90af89df

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

diffstat:
 py-pysam/Makefile                   |  46 +++---
 py-pysam/PLIST                      | 274 +++++++++++++++++++++++++++++++++++-
 py-pysam/distinfo                   |   9 +-
 py-pysam/patches/patch-cy__build.py |  31 ----
 py-pysam/patches/patch-setup.py     |   2 +-
 5 files changed, 297 insertions(+), 65 deletions(-)

diffs:
diff --git a/py-pysam/Makefile b/py-pysam/Makefile
index 118fec2f4a..3628b1225c 100644
--- a/py-pysam/Makefile
+++ b/py-pysam/Makefile
@@ -1,34 +1,30 @@
 # $NetBSD$
-
-GITHUB_PROJECT=	pysam
-GITHUB_TAG=	refs/tags/v0.16.0.1
-DISTNAME=	v0.16.0.1
-PKGNAME=	${PYPKGPREFIX}-${GITHUB_PROJECT}-${DISTNAME:S,^v,,}
-CATEGORIES=	biology python
-MASTER_SITES=	${MASTER_SITE_GITHUB:=pysam-developers/}
-DIST_SUBDIR=	${GITHUB_PROJECT}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://github.com/pysam-developers/pysam/
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Thu Jul 27 18:54:54 CDT 2023               #
+###########################################################
+
+DISTNAME=	pysam-0.21.0
+PKGNAME=	${PYPKGPREFIX}-pysam-0.21.0
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_PYPI:=p/pysam/}
+
+OWNER=		bacon%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/pysam-developers/pysam
 COMMENT=	Python module for reading, manipulating and writing genomic data sets
 LICENSE=	mit
 
-WRKSRC=		${WRKDIR}/${GITHUB_PROJECT}-${PKGVERSION_NOREV}
 USE_TOOLS+=	gmake
+MAKE_ENV+=	HTSLIB_MODE=external \
+		HTSLIB_LIBRARY_DIR=${PREFIX}/lib \
+		HTSLIB_INCLUDE_DIR=${PREFIX}/include
 
-EGG_NAME=	${GITHUB_PROJECT}-${PKGVERSION_NOREV}
-
-MAKE_ENV+=	PYSITELIB=${PYSITELIB}
-
-MAKE_ENV+=	HTSLIB_MODE=external
-MAKE_ENV+=	HTSLIB_INCLUDE_DIR=${BUILDLINK_PREFIX.htslib}/include
-MAKE_ENV+=	HTSLIB_LIBRARY_DIR=${BUILDLINK_PREFIX.htslib}/lib
+post-install:
+	${STRIP} ${DESTDIR}${PREFIX}/${PYSITELIB}/pysam/lib*.so
 
-# FIXME: Why is this necessary?
-LDFLAGS+=	-L${DESTDIR}${PREFIX}/${PYSITELIB}/pysam
-LDFLAGS+=	${COMPILER_RPATH_FLAG}${PREFIX}/${PYSITELIB}/pysam
-
-.include "../../biology/htslib/buildlink3.mk"
-.include "../../devel/py-cython/buildlink3.mk"
 .include "../../lang/python/egg.mk"
+.include "../../biology/htslib/buildlink3.mk"
+# CentOS doesn't have zlib in the base, so uncomment if needed.
+# .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/py-pysam/PLIST b/py-pysam/PLIST
index 3bba2177ca..e234288749 100644
--- a/py-pysam/PLIST
+++ b/py-pysam/PLIST
@@ -3,6 +3,7 @@ ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
 ${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
 ${PYSITELIB}/${EGG_INFODIR}/top_level.txt
 ${PYSITELIB}/pysam/Pileup.py
 ${PYSITELIB}/pysam/Pileup.pyc
@@ -18,77 +19,343 @@ ${PYSITELIB}/pysam/config.py
 ${PYSITELIB}/pysam/config.pyc
 ${PYSITELIB}/pysam/config.pyo
 ${PYSITELIB}/pysam/csamtools_util.h
+${PYSITELIB}/pysam/htslib_util.c
 ${PYSITELIB}/pysam/htslib_util.h
 ${PYSITELIB}/pysam/include/__init__.py
 ${PYSITELIB}/pysam/include/__init__.pyc
 ${PYSITELIB}/pysam/include/__init__.pyo
+${PYSITELIB}/pysam/include/bcftools/HMM.c
+${PYSITELIB}/pysam/include/bcftools/HMM.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/HMM.h
+${PYSITELIB}/pysam/include/bcftools/LICENSE
+${PYSITELIB}/pysam/include/bcftools/README
+${PYSITELIB}/pysam/include/bcftools/abuf.c
+${PYSITELIB}/pysam/include/bcftools/abuf.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/abuf.h
+${PYSITELIB}/pysam/include/bcftools/bam2bcf.c
+${PYSITELIB}/pysam/include/bcftools/bam2bcf.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/bam2bcf.h
+${PYSITELIB}/pysam/include/bcftools/bam2bcf_iaux.c
+${PYSITELIB}/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/bam2bcf_indel.c
+${PYSITELIB}/pysam/include/bcftools/bam2bcf_indel.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/bam_sample.c
+${PYSITELIB}/pysam/include/bcftools/bam_sample.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/bam_sample.h
 ${PYSITELIB}/pysam/include/bcftools/bcftools.h
+${PYSITELIB}/pysam/include/bcftools/bcftools.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/bcftools.pysam.h
+${PYSITELIB}/pysam/include/bcftools/bin.c
+${PYSITELIB}/pysam/include/bcftools/bin.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/bin.h
 ${PYSITELIB}/pysam/include/bcftools/call.h
+${PYSITELIB}/pysam/include/bcftools/ccall.c
+${PYSITELIB}/pysam/include/bcftools/ccall.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/cigar_state.h
+${PYSITELIB}/pysam/include/bcftools/cols.c
+${PYSITELIB}/pysam/include/bcftools/cols.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/cols.h
 ${PYSITELIB}/pysam/include/bcftools/config.h
+${PYSITELIB}/pysam/include/bcftools/consensus.c
+${PYSITELIB}/pysam/include/bcftools/consensus.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/convert.c
+${PYSITELIB}/pysam/include/bcftools/convert.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/convert.h
+${PYSITELIB}/pysam/include/bcftools/csq.c
+${PYSITELIB}/pysam/include/bcftools/csq.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/dbuf.h
+${PYSITELIB}/pysam/include/bcftools/dist.c
+${PYSITELIB}/pysam/include/bcftools/dist.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/dist.h
+${PYSITELIB}/pysam/include/bcftools/em.c
+${PYSITELIB}/pysam/include/bcftools/em.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/extsort.c
+${PYSITELIB}/pysam/include/bcftools/extsort.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/extsort.h
+${PYSITELIB}/pysam/include/bcftools/filter.c
+${PYSITELIB}/pysam/include/bcftools/filter.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/filter.h
+${PYSITELIB}/pysam/include/bcftools/gvcf.c
+${PYSITELIB}/pysam/include/bcftools/gvcf.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/gvcf.h
+${PYSITELIB}/pysam/include/bcftools/hclust.c
+${PYSITELIB}/pysam/include/bcftools/hclust.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/hclust.h
 ${PYSITELIB}/pysam/include/bcftools/hex.h
 ${PYSITELIB}/pysam/include/bcftools/khash_str2str.h
 ${PYSITELIB}/pysam/include/bcftools/kheap.h
+${PYSITELIB}/pysam/include/bcftools/kmin.c
+${PYSITELIB}/pysam/include/bcftools/kmin.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/kmin.h
+${PYSITELIB}/pysam/include/bcftools/main.c
+${PYSITELIB}/pysam/include/bcftools/main.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/mcall.c
+${PYSITELIB}/pysam/include/bcftools/mcall.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/mpileup.c
+${PYSITELIB}/pysam/include/bcftools/mpileup.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/mw.h
+${PYSITELIB}/pysam/include/bcftools/ploidy.c
+${PYSITELIB}/pysam/include/bcftools/ploidy.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/ploidy.h
+${PYSITELIB}/pysam/include/bcftools/prob1.c
+${PYSITELIB}/pysam/include/bcftools/prob1.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/prob1.h
 ${PYSITELIB}/pysam/include/bcftools/rbuf.h
+${PYSITELIB}/pysam/include/bcftools/read_consensus.c
+${PYSITELIB}/pysam/include/bcftools/read_consensus.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/read_consensus.h
+${PYSITELIB}/pysam/include/bcftools/regidx.c
+${PYSITELIB}/pysam/include/bcftools/regidx.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/regidx.h
+${PYSITELIB}/pysam/include/bcftools/reheader.c
+${PYSITELIB}/pysam/include/bcftools/reheader.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/smpl_ilist.c
+${PYSITELIB}/pysam/include/bcftools/smpl_ilist.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/smpl_ilist.h
+${PYSITELIB}/pysam/include/bcftools/str_finder.c
+${PYSITELIB}/pysam/include/bcftools/str_finder.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/str_finder.h
+${PYSITELIB}/pysam/include/bcftools/tabix.c
+${PYSITELIB}/pysam/include/bcftools/tabix.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/tsv2vcf.c
+${PYSITELIB}/pysam/include/bcftools/tsv2vcf.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/tsv2vcf.h
+${PYSITELIB}/pysam/include/bcftools/utlist.h
 ${PYSITELIB}/pysam/include/bcftools/variantkey.h
+${PYSITELIB}/pysam/include/bcftools/vcfannotate.c
+${PYSITELIB}/pysam/include/bcftools/vcfannotate.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfbuf.c
+${PYSITELIB}/pysam/include/bcftools/vcfbuf.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/vcfbuf.h
+${PYSITELIB}/pysam/include/bcftools/vcfcall.c
+${PYSITELIB}/pysam/include/bcftools/vcfcall.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfcnv.c
+${PYSITELIB}/pysam/include/bcftools/vcfcnv.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfconcat.c
+${PYSITELIB}/pysam/include/bcftools/vcfconcat.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfconvert.c
+${PYSITELIB}/pysam/include/bcftools/vcfconvert.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcffilter.c
+${PYSITELIB}/pysam/include/bcftools/vcffilter.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfgtcheck.c
+${PYSITELIB}/pysam/include/bcftools/vcfgtcheck.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfhead.c
+${PYSITELIB}/pysam/include/bcftools/vcfhead.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfindex.c
+${PYSITELIB}/pysam/include/bcftools/vcfindex.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfisec.c
+${PYSITELIB}/pysam/include/bcftools/vcfisec.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfmerge.c
+${PYSITELIB}/pysam/include/bcftools/vcfmerge.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfnorm.c
+${PYSITELIB}/pysam/include/bcftools/vcfnorm.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfplugin.c
+${PYSITELIB}/pysam/include/bcftools/vcfplugin.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfquery.c
+${PYSITELIB}/pysam/include/bcftools/vcfquery.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfroh.c
+${PYSITELIB}/pysam/include/bcftools/vcfroh.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfsom.c
+${PYSITELIB}/pysam/include/bcftools/vcfsom.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfsort.c
+${PYSITELIB}/pysam/include/bcftools/vcfsort.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfstats.c
+${PYSITELIB}/pysam/include/bcftools/vcfstats.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcfview.c
+${PYSITELIB}/pysam/include/bcftools/vcfview.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/vcmp.c
+${PYSITELIB}/pysam/include/bcftools/vcmp.c.pysam.c
 ${PYSITELIB}/pysam/include/bcftools/vcmp.h
+${PYSITELIB}/pysam/include/bcftools/version.c
+${PYSITELIB}/pysam/include/bcftools/version.c.pysam.c
+${PYSITELIB}/pysam/include/bcftools/version.sh
+${PYSITELIB}/pysam/include/samtools/LICENSE
+${PYSITELIB}/pysam/include/samtools/README
+${PYSITELIB}/pysam/include/samtools/amplicon_stats.c
+${PYSITELIB}/pysam/include/samtools/amplicon_stats.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam.c
+${PYSITELIB}/pysam/include/samtools/bam.c.pysam.c
 ${PYSITELIB}/pysam/include/samtools/bam.h
-${PYSITELIB}/pysam/include/samtools/bam2bcf.h
-${PYSITELIB}/pysam/include/samtools/bam_endian.h
+${PYSITELIB}/pysam/include/samtools/bam2depth.c
+${PYSITELIB}/pysam/include/samtools/bam2depth.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_addrprg.c
+${PYSITELIB}/pysam/include/samtools/bam_addrprg.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_ampliconclip.c
+${PYSITELIB}/pysam/include/samtools/bam_ampliconclip.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_ampliconclip.h
+${PYSITELIB}/pysam/include/samtools/bam_aux.c
+${PYSITELIB}/pysam/include/samtools/bam_aux.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_cat.c
+${PYSITELIB}/pysam/include/samtools/bam_cat.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_color.c
+${PYSITELIB}/pysam/include/samtools/bam_color.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_consensus.c
+${PYSITELIB}/pysam/include/samtools/bam_consensus.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_fastq.c
+${PYSITELIB}/pysam/include/samtools/bam_fastq.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_flags.c
+${PYSITELIB}/pysam/include/samtools/bam_flags.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_import.c
+${PYSITELIB}/pysam/include/samtools/bam_import.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_index.c
+${PYSITELIB}/pysam/include/samtools/bam_index.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_lpileup.c
+${PYSITELIB}/pysam/include/samtools/bam_lpileup.c.pysam.c
 ${PYSITELIB}/pysam/include/samtools/bam_lpileup.h
+${PYSITELIB}/pysam/include/samtools/bam_markdup.c
+${PYSITELIB}/pysam/include/samtools/bam_markdup.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_mate.c
+${PYSITELIB}/pysam/include/samtools/bam_mate.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_md.c
+${PYSITELIB}/pysam/include/samtools/bam_md.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_plbuf.c
+${PYSITELIB}/pysam/include/samtools/bam_plbuf.c.pysam.c
 ${PYSITELIB}/pysam/include/samtools/bam_plbuf.h
+${PYSITELIB}/pysam/include/samtools/bam_plcmd.c
+${PYSITELIB}/pysam/include/samtools/bam_plcmd.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_quickcheck.c
+${PYSITELIB}/pysam/include/samtools/bam_quickcheck.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_reheader.c
+${PYSITELIB}/pysam/include/samtools/bam_reheader.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_rmdup.c
+${PYSITELIB}/pysam/include/samtools/bam_rmdup.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_rmdupse.c
+${PYSITELIB}/pysam/include/samtools/bam_rmdupse.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_samples.c
+${PYSITELIB}/pysam/include/samtools/bam_samples.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_sort.c
+${PYSITELIB}/pysam/include/samtools/bam_sort.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_split.c
+${PYSITELIB}/pysam/include/samtools/bam_split.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bam_stat.c
+${PYSITELIB}/pysam/include/samtools/bam_stat.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bamshuf.c
+${PYSITELIB}/pysam/include/samtools/bamshuf.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bamtk.c
+${PYSITELIB}/pysam/include/samtools/bamtk.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bedcov.c
+${PYSITELIB}/pysam/include/samtools/bedcov.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/bedidx.c
+${PYSITELIB}/pysam/include/samtools/bedidx.c.pysam.c
 ${PYSITELIB}/pysam/include/samtools/bedidx.h
 ${PYSITELIB}/pysam/include/samtools/config.h
-${PYSITELIB}/pysam/include/samtools/sam.h
+${PYSITELIB}/pysam/include/samtools/consensus_pileup.c
+${PYSITELIB}/pysam/include/samtools/consensus_pileup.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/consensus_pileup.h
+${PYSITELIB}/pysam/include/samtools/coverage.c
+${PYSITELIB}/pysam/include/samtools/coverage.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/cram_size.c
+${PYSITELIB}/pysam/include/samtools/cram_size.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/cut_target.c
+${PYSITELIB}/pysam/include/samtools/cut_target.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/dict.c
+${PYSITELIB}/pysam/include/samtools/dict.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/faidx.c
+${PYSITELIB}/pysam/include/samtools/faidx.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/lz4/LICENSE
+${PYSITELIB}/pysam/include/samtools/lz4/lz4.c
+${PYSITELIB}/pysam/include/samtools/lz4/lz4.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/lz4/lz4.h
+${PYSITELIB}/pysam/include/samtools/padding.c
+${PYSITELIB}/pysam/include/samtools/padding.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/phase.c
+${PYSITELIB}/pysam/include/samtools/phase.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/reference.c
+${PYSITELIB}/pysam/include/samtools/reference.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/reset.c
+${PYSITELIB}/pysam/include/samtools/reset.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/sam_opts.c
+${PYSITELIB}/pysam/include/samtools/sam_opts.c.pysam.c
 ${PYSITELIB}/pysam/include/samtools/sam_opts.h
+${PYSITELIB}/pysam/include/samtools/sam_utils.c
+${PYSITELIB}/pysam/include/samtools/sam_utils.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/sam_utils.h
+${PYSITELIB}/pysam/include/samtools/sam_view.c
+${PYSITELIB}/pysam/include/samtools/sam_view.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/sample.c
+${PYSITELIB}/pysam/include/samtools/sample.c.pysam.c
 ${PYSITELIB}/pysam/include/samtools/sample.h
 ${PYSITELIB}/pysam/include/samtools/samtools.h
+${PYSITELIB}/pysam/include/samtools/samtools.pysam.c
 ${PYSITELIB}/pysam/include/samtools/samtools.pysam.h
+${PYSITELIB}/pysam/include/samtools/samtools_config_vars.h
+${PYSITELIB}/pysam/include/samtools/splaysort.h
+${PYSITELIB}/pysam/include/samtools/stats.c
+${PYSITELIB}/pysam/include/samtools/stats.c.pysam.c
+${PYSITELIB}/pysam/include/samtools/stats_isize.c
+${PYSITELIB}/pysam/include/samtools/stats_isize.c.pysam.c
 ${PYSITELIB}/pysam/include/samtools/stats_isize.h
+${PYSITELIB}/pysam/include/samtools/tmp_file.c
+${PYSITELIB}/pysam/include/samtools/tmp_file.c.pysam.c
 ${PYSITELIB}/pysam/include/samtools/tmp_file.h
+${PYSITELIB}/pysam/include/samtools/version.sh
+${PYSITELIB}/pysam/libcalignedsegment.c
 ${PYSITELIB}/pysam/libcalignedsegment.pxd
+${PYSITELIB}/pysam/libcalignedsegment.pyi
+${PYSITELIB}/pysam/libcalignedsegment.pyx
 ${PYSITELIB}/pysam/libcalignedsegment.so
+${PYSITELIB}/pysam/libcalignmentfile.c
 ${PYSITELIB}/pysam/libcalignmentfile.pxd
+${PYSITELIB}/pysam/libcalignmentfile.pyi
+${PYSITELIB}/pysam/libcalignmentfile.pyx
 ${PYSITELIB}/pysam/libcalignmentfile.so
+${PYSITELIB}/pysam/libcbcf.c
 ${PYSITELIB}/pysam/libcbcf.pxd
+${PYSITELIB}/pysam/libcbcf.pyi
+${PYSITELIB}/pysam/libcbcf.pyx
 ${PYSITELIB}/pysam/libcbcf.so
+${PYSITELIB}/pysam/libcbcftools.c
 ${PYSITELIB}/pysam/libcbcftools.pxd
+${PYSITELIB}/pysam/libcbcftools.pyi
+${PYSITELIB}/pysam/libcbcftools.pyx
 ${PYSITELIB}/pysam/libcbcftools.so
+${PYSITELIB}/pysam/libcbgzf.c
+${PYSITELIB}/pysam/libcbgzf.pyi
+${PYSITELIB}/pysam/libcbgzf.pyx
 ${PYSITELIB}/pysam/libcbgzf.so
+${PYSITELIB}/pysam/libcfaidx.c
 ${PYSITELIB}/pysam/libcfaidx.pxd
+${PYSITELIB}/pysam/libcfaidx.pyi
+${PYSITELIB}/pysam/libcfaidx.pyx
 ${PYSITELIB}/pysam/libcfaidx.so
+${PYSITELIB}/pysam/libchtslib.c
 ${PYSITELIB}/pysam/libchtslib.pxd
+${PYSITELIB}/pysam/libchtslib.pyi
+${PYSITELIB}/pysam/libchtslib.pyx
 ${PYSITELIB}/pysam/libchtslib.so
+${PYSITELIB}/pysam/libcsamfile.c
 ${PYSITELIB}/pysam/libcsamfile.pxd
+${PYSITELIB}/pysam/libcsamfile.pyi
+${PYSITELIB}/pysam/libcsamfile.pyx
 ${PYSITELIB}/pysam/libcsamfile.so
+${PYSITELIB}/pysam/libcsamtools.c
 ${PYSITELIB}/pysam/libcsamtools.pxd
+${PYSITELIB}/pysam/libcsamtools.pyi
+${PYSITELIB}/pysam/libcsamtools.pyx
 ${PYSITELIB}/pysam/libcsamtools.so
+${PYSITELIB}/pysam/libctabix.c
 ${PYSITELIB}/pysam/libctabix.pxd
+${PYSITELIB}/pysam/libctabix.pyi
+${PYSITELIB}/pysam/libctabix.pyx
 ${PYSITELIB}/pysam/libctabix.so
+${PYSITELIB}/pysam/libctabixproxies.c
 ${PYSITELIB}/pysam/libctabixproxies.pxd
+${PYSITELIB}/pysam/libctabixproxies.pyi
+${PYSITELIB}/pysam/libctabixproxies.pyx
 ${PYSITELIB}/pysam/libctabixproxies.so
+${PYSITELIB}/pysam/libcutils.c
 ${PYSITELIB}/pysam/libcutils.pxd
+${PYSITELIB}/pysam/libcutils.pyi
+${PYSITELIB}/pysam/libcutils.pyx
 ${PYSITELIB}/pysam/libcutils.so
+${PYSITELIB}/pysam/libcvcf.c
 ${PYSITELIB}/pysam/libcvcf.pxd
+${PYSITELIB}/pysam/libcvcf.pyi
+${PYSITELIB}/pysam/libcvcf.pyx
 ${PYSITELIB}/pysam/libcvcf.so
+${PYSITELIB}/pysam/py.typed
 ${PYSITELIB}/pysam/pysam_stream.h
+${PYSITELIB}/pysam/pysam_util.c
 ${PYSITELIB}/pysam/pysam_util.h
 ${PYSITELIB}/pysam/samtools.py
 ${PYSITELIB}/pysam/samtools.pyc
@@ -99,4 +366,5 @@ ${PYSITELIB}/pysam/utils.pyo
 ${PYSITELIB}/pysam/version.h
 ${PYSITELIB}/pysam/version.py
 ${PYSITELIB}/pysam/version.pyc
+${PYSITELIB}/pysam/version.pyi
 ${PYSITELIB}/pysam/version.pyo
diff --git a/py-pysam/distinfo b/py-pysam/distinfo
index 412cba2986..6869cec9f0 100644
--- a/py-pysam/distinfo
+++ b/py-pysam/distinfo
@@ -1,7 +1,6 @@
 $NetBSD$
 
-RMD160 (pysam/v0.16.0.1.tar.gz) = 7a980c0bd6edac6bdd9103db0fc6f540b0db6619
-SHA512 (pysam/v0.16.0.1.tar.gz) = 5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28
-Size (pysam/v0.16.0.1.tar.gz) = 3294073 bytes
-SHA1 (patch-cy__build.py) = 1bb61fc7fcdfbb9305150ff437ba614f57b3756e
-SHA1 (patch-setup.py) = 368c4b99c1f8103d34096145f7badd9310736554
+BLAKE2s (pysam-0.21.0.tar.gz) = 6aa54861ae9e5f32643ab3c8599d342d2b2ee68d589372ceb6ea968521f8661c
+SHA512 (pysam-0.21.0.tar.gz) = e42355ee02e5b6a8dbd4e94e46e7a70ce4f8e3d3d8c17440d34e420b0fa4730dce60a74078098a2d7d34a26110d694e59178c38de431b9c61d46b1e5d32ded19
+Size (pysam-0.21.0.tar.gz) = 4052537 bytes
+SHA1 (patch-setup.py) = be715207431b0fbafe4e87cf4cdc8ad81dffb31e
diff --git a/py-pysam/patches/patch-cy__build.py b/py-pysam/patches/patch-cy__build.py
deleted file mode 100644
index c0ca677cb9..0000000000
--- a/py-pysam/patches/patch-cy__build.py
+++ /dev/null
@@ -1,31 +0,0 @@
-$NetBSD$
-
-On Darwin, set LC_ID_DYLIB to ${PREFIX}/${PYSITELIB}/pysam/...
-to ensure libraries are found at runtime.  Avoid use of @rpath.
-
---- cy_build.py.orig	2018-02-07 21:01:12.000000000 +0000
-+++ cy_build.py
-@@ -60,20 +60,16 @@ class cy_build_ext(build_ext):
-             ext.library_dirs.append(os.path.join(self.build_lib, "pysam"))
- 
-         if sys.platform == 'darwin':
--            # The idea is to give shared libraries an install name of the form
--            # `@rpath/<library-name.so>`, and to set the rpath equal to
--            # @loader_path. This will allow Python packages to find the library
--            # in the expected place, while still giving enough flexibility to
--            # external applications to link against the library.
-+            # Set LC_ID_DYLIB to ${PREFIX}/${PYSITELIB}/pysam/... to ensure
-+            # libraries are found at runtime.  Avoid use of @rpath.
-             relative_module_path = ext.name.replace(".", os.sep) + get_config_vars()["SO"]
-             library_path = os.path.join(
--                "@rpath", os.path.basename(relative_module_path)
-+                os.environ["PREFIX"], os.environ["PYSITELIB"], "pysam", os.path.basename(relative_module_path)
-             )
- 
-             if not ext.extra_link_args:
-                 ext.extra_link_args = []
-             ext.extra_link_args += ['-dynamiclib',
--                                    '-rpath', '@loader_path',
-                                     '-Wl,-headerpad_max_install_names',
-                                     '-Wl,-install_name,%s' % library_path,
-                                     '-Wl,-x']
diff --git a/py-pysam/patches/patch-setup.py b/py-pysam/patches/patch-setup.py
index 9231af0479..c87e10c59c 100644
--- a/py-pysam/patches/patch-setup.py
+++ b/py-pysam/patches/patch-setup.py
@@ -1,6 +1,6 @@
 $NetBSD$
 
-# Portability
+# Cannot use BSD make
 
 --- setup.py.orig	2017-04-19 05:48:10 UTC
 +++ setup.py
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