Commit 8dac8123 authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 1.10

parent fc3ddb2b

LICENSE

+1 −1
Original line number Diff line number Diff line 
The MIT/Expat License



Copyright (C) 2008-2018 Genome Research Ltd.

Copyright (C) 2008-2019 Genome Research Ltd.



Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

Makefile

+51 −45
Original line number Diff line number Diff line 
# Makefile for samtools, utilities for the Sequence Alignment/Map format.

#

#    Copyright (C) 2008-2017 Genome Research Ltd.

#    Copyright (C) 2008-2019 Genome Research Ltd.

#    Portions copyright (C) 2010-2012 Broad Institute.

#

# Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -35,13 +35,13 @@ LZ4_LDFLAGS = -L$(LZ4DIR) 






LOBJS=      bam_aux.o bam.o bam_import.o sam.o \

            sam_header.o bam_plbuf.o

AOBJS=      bam_index.o bam_plcmd.o sam_view.o \

LOBJS=      bam_aux.o bam.o sam.o \

            bam_plbuf.o

AOBJS=      bam_index.o bam_plcmd.o sam_view.o bam_fastq.o \

            bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o \

            bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \

            bamtk.o bam2bcf.o bam2bcf_indel.o sample.o \

            cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \

            cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o \

            faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o \

            bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \

            bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o
@@ -77,8 +77,7 @@ MISC_SCRIPTS = \ 
	misc/interpolate_sam.pl misc/novo2sam.pl \

	misc/plot-bamstats misc/psl2sam.pl \

	misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl \

	misc/soap2sam.pl \

	misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl

	misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl



TEST_PROGRAMS = \

	test/merge/test_bam_translate \
@@ -158,55 +157,62 @@ bedidx_h = bedidx.h $(htslib_hts_h) 
sam_h = sam.h $(htslib_sam_h) $(bam_h)

sam_opts_h = sam_opts.h $(htslib_hts_h)

sample_h = sample.h $(htslib_kstring_h)

samtools_h = samtools.h $(htslib_hts_defs_h) $(htslib_sam_h)

stats_isize_h = stats_isize.h $(htslib_khash_h)

tmp_file_h = tmp_file.h $(htslib_sam_h) $(LZ4DIR)/lz4.h



bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h

bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h)

bam2bcf.o: bam2bcf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h)

bam2bcf_indel.o: bam2bcf_indel.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam2bcf_h) $(htslib_khash_h) $(htslib_ksort_h)

bam2depth.o: bam2depth.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h)

bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(htslib_thread_pool_h) $(sam_opts_h)

bam2depth.o: bam2depth.c config.h $(htslib_sam_h) $(samtools_h) $(bedidx_h) $(sam_opts_h)

coverage.o: coverage.c config.h $(htslib_sam_h) $(htslib_hts_h) $(samtools_h) $(sam_opts_h)

bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) $(samtools_h) $(htslib_thread_pool_h) $(sam_opts_h)

bam_aux.o: bam_aux.c config.h $(bam_h)

bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) samtools.h

bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_kstring_h) $(samtools_h) $(sam_opts_h)

bam_color.o: bam_color.c config.h $(bam_h)

bam_import.o: bam_import.c config.h $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h)

bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h $(sam_opts_h)

bam_fastq.o: bam_fastq.c config.h $(htslib_sam_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_bgzf_h) $(htslib_thread_pool_h) $(samtools_h) $(sam_opts_h)

bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) $(samtools_h) $(sam_opts_h)

bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h)

bam_mate.o: bam_mate.c config.h $(htslib_thread_pool_h) $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) samtools.h

bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_thread_pool_h) $(sam_opts_h) samtools.h

bam_mate.o: bam_mate.c config.h $(htslib_thread_pool_h) $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) $(samtools_h)

bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_thread_pool_h) $(sam_opts_h) $(samtools_h)

bam_plbuf.o: bam_plbuf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)

bam_plcmd.o: bam_plcmd.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)

bam_plcmd.o: bam_plcmd.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_klist_h) $(htslib_khash_str2int_h) $(samtools_h) $(bedidx_h) $(sam_opts_h) $(bam2bcf_h) $(sample_h)

bam_quickcheck.o: bam_quickcheck.c config.h $(htslib_hts_h) $(htslib_sam_h)

bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h

bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h)

bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) samtools.h

bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_hts_os_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) samtools.h

bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(htslib_cram_h) $(htslib_thread_pool_h) $(sam_opts_h) samtools.h

bam_stat.o: bam_stat.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h)

bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) samtools.h $(sam_opts_h)

bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) $(samtools_h)

bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) $(samtools_h) $(bam_h) $(htslib_khash_h)

bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) $(samtools_h)

bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_hts_os_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(htslib_hts_endian_h) $(sam_opts_h) $(samtools_h)

bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(htslib_cram_h) $(htslib_thread_pool_h) $(sam_opts_h) $(samtools_h)

bam_stat.o: bam_stat.c config.h $(htslib_sam_h) $(samtools_h) $(sam_opts_h)

bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(samtools_h) $(sam_opts_h)

bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h)

bam_tview_html.o: bam_tview_html.c config.h $(bam_tview_h)

bam_flags.o: bam_flags.c config.h $(htslib_sam_h)

bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(htslib_thread_pool_h) $(sam_opts_h) $(htslib_khash_h)

bamtk.o: bamtk.c config.h $(htslib_hts_h) samtools.h version.h

bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_thread_pool_h) $(sam_opts_h) $(htslib_kseq_h)

bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) $(samtools_h) $(htslib_thread_pool_h) $(sam_opts_h) $(htslib_khash_h)

bamtk.o: bamtk.c config.h $(htslib_hts_h) $(samtools_h) version.h

bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_thread_pool_h) $(samtools_h) $(sam_opts_h) $(htslib_kseq_h)

bedidx.o: bedidx.c config.h $(bedidx_h) $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h)

cut_target.o: cut_target.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) samtools.h $(sam_opts_h)

cut_target.o: cut_target.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(samtools_h) $(sam_opts_h)

dict.o: dict.c config.h $(htslib_kseq_h) $(htslib_hts_h)

faidx.o: faidx.c config.h $(htslib_faidx_h) $(htslib_hts_h) $(htslib_hfile_h) $(htslib_kstring_h) samtools.h

padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) samtools.h

phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h $(htslib_hts_os_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h)

faidx.o: faidx.c config.h $(htslib_faidx_h) $(htslib_hts_h) $(htslib_hfile_h) $(htslib_kstring_h) $(samtools_h)

padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) $(sam_opts_h) $(samtools_h)

phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) $(samtools_h) $(htslib_hts_os_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h)

sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h)

sam_header.o: sam_header.c config.h sam_header.h $(htslib_khash_h)

sam_opts.o: sam_opts.c config.h $(sam_opts_h)

sam_utils.o: sam_utils.c config.h samtools.h

sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_thread_pool_h) $(htslib_bgzf_h) samtools.h $(sam_opts_h) $(bedidx_h)

sam_utils.o: sam_utils.c config.h $(samtools_h)

sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_khash_h) $(htslib_thread_pool_h) $(samtools_h) $(sam_opts_h) $(bedidx_h)

sample.o: sample.c config.h $(sample_h) $(htslib_khash_h)

stats_isize.o: stats_isize.c config.h $(stats_isize_h) $(htslib_khash_h)

stats.o: stats.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) $(stats_isize_h) $(sam_opts_h) $(bedidx_h)

bam_markdup.o: bam_markdup.c config.h $(htslib_thread_pool_h) $(htslib_sam_h) $(sam_opts_h) samtools.h $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(tmp_file_h)

stats.o: stats.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) $(htslib_hts_defs_h) $(htslib_khash_str2int_h) $(samtools_h) $(htslib_khash_h) $(htslib_kstring_h) $(stats_isize_h) $(sam_opts_h) $(bedidx_h)

bam_markdup.o: bam_markdup.c config.h $(htslib_thread_pool_h) $(htslib_sam_h) $(sam_opts_h) $(samtools_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(tmp_file_h)

tmp_file.o: tmp_file.c config.h $(tmp_file_h) $(htslib_sam_h)



# Maintainer source code checks

# - copyright boilerplate presence

# - tab and trailing space detection

maintainer-check:

	test/maintainer/check_copyright.pl .

	test/maintainer/check_spaces.pl .



# test programs
@@ -217,26 +223,26 @@ tmp_file.o: tmp_file.c config.h $(tmp_file_h) $(htslib_sam_h) 
# If using MSYS, avoid poor shell expansion via:

#    MSYS2_ARG_CONV_EXCL="*" make check

check test: samtools $(BGZIP) $(TEST_PROGRAMS)

	test/split/test_count_rg

	test/split/test_expand_format_string

	test/split/test_filter_header_rg

	test/split/test_parse_args

	REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) $${TEST_OPTS:-}

	test/merge/test_bam_translate test/merge/test_bam_translate.tmp

	test/merge/test_rtrans_build

	test/merge/test_trans_tbl_init

	cd test/mpileup && ./regression.sh mpileup.reg

	cd test/mpileup && ./regression.sh depth.reg

	test/split/test_count_rg

	test/split/test_expand_format_string

	test/split/test_filter_header_rg

	test/split/test_parse_args





test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB)

	$(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread



test/merge/test_rtrans_build: test/merge/test_rtrans_build.o libst.a $(HTSLIB)

	$(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread

test/merge/test_rtrans_build: test/merge/test_rtrans_build.o test/test.o libst.a $(HTSLIB)

	$(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread



test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o libst.a $(HTSLIB)

	$(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread

test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o test/test.o libst.a $(HTSLIB)

	$(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread



test/split/test_count_rg: test/split/test_count_rg.o test/test.o libst.a $(HTSLIB)

	$(CC) $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
@@ -260,7 +266,7 @@ test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c config.h bam_sort 
test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c config.h bam_sort.o

test/split/test_count_rg.o: test/split/test_count_rg.c config.h bam_split.o $(test_test_h)

test/split/test_expand_format_string.o: test/split/test_expand_format_string.c config.h bam_split.o $(test_test_h)

test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h bam_split.o $(test_test_h)

test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h $(test_test_h) $(samtools_h) $(htslib_kstring_h)

test/split/test_parse_args.o: test/split/test_parse_args.c config.h bam_split.o $(test_test_h)

test/test.o: test/test.c config.h $(htslib_sam_h) $(test_test_h)

test/vcf-miniview.o: test/vcf-miniview.c config.h $(htslib_vcf_h)
@@ -303,7 +309,7 @@ install: $(PROGRAMS) $(MISC_PROGRAMS) 
	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)

	$(INSTALL_PROGRAM) $(MISC_PROGRAMS) $(DESTDIR)$(misc_bindir)

	$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)

	$(INSTALL_MAN) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)

	$(INSTALL_MAN) doc/samtools*.1 misc/wgsim.1 $(DESTDIR)$(man1dir)





testclean:

Makefile.mingw

deleted100644 → 0
+0 −63
Original line number Diff line number Diff line 
CC=			gcc.exe

AR=			ar.exe

CFLAGS=		-g -Wall -O2

DFLAGS=		-D_USE_KNETFILE -D_CURSES_LIB=2

KNETFILE_O=	knetfile.o

LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\

			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \

			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bedidx.o

AOBJS=		bam_tview.o bam_plcmd.o sam_view.o \

			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o	\

			bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \

			cut_target.o phase.o bam_cat.o bam2depth.o

BCFOBJS=	bcftools/bcf.o bcftools/fet.o bcftools/bcf2qcall.o bcftools/bcfutils.o \

			bcftools/call1.o bcftools/index.o bcftools/kfunc.o bcftools/em.o \

			bcftools/kmin.o bcftools/prob1.o bcftools/vcf.o bcftools/mut.o

PROG=		samtools.exe bcftools.exe

INCLUDES=	-I. -Iwin32

SUBDIRS=	.

LIBPATH=



.SUFFIXES:.c .o



.c.o:

		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@



all:$(PROG)



.PHONY:all lib clean cleanlocal

.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur



lib:libbam.a



libbam.a:$(LOBJS)

		$(AR) -cru $@ $(LOBJS)



samtools.exe:$(AOBJS) libbam.a $(BCFOBJS)

		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(BCFOBJS) $(LIBPATH) -lm -L. -lbam -Lwin32 -lz -lcurses -lws2_32



bcftools.exe:$(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o

		$(CC) $(CFLAGS) -o $@ $(BCFOBJS) bcftools/main.o kstring.o bgzf.o knetfile.o bedidx.o -lm -Lwin32 -lz -lws2_32



razip.o:razf.h

bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h

sam.o:sam.h bam.h

bam_import.o:bam.h kseq.h khash.h razf.h

bam_pileup.o:bam.h razf.h ksort.h

bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h

bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h

bam_lpileup.o:bam.h ksort.h

bam_tview.o:bam.h faidx.h

bam_sort.o:bam.h ksort.h razf.h

bam_md.o:bam.h faidx.h

sam_header.o:sam_header.h khash.h

bcf.o:bcftools/bcf.h

bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h

bam2bcf_indel.o:bam2bcf.h

errmod.o:errmod.h



faidx.o:faidx.h razf.h khash.h

faidx_main.o:faidx.h razf.h



clean:

		rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib

NEWS

+277 −4

File changed.

Preview size limit exceeded, changes collapsed.

README

+5 −5
Original line number Diff line number Diff line
@@ -9,7 +9,7 @@ Building samtools 
The typical simple case of building Samtools using the HTSlib bundled within

this Samtools release tarball is done as follows:



    cd .../samtools-1.9 # Within the unpacked release directory

    cd .../samtools-1.10 # Within the unpacked release directory

    ./configure

    make
@@ -21,7 +21,7 @@ install samtools etc properly into a directory of your choosing. Building for 
installation using the HTSlib bundled within this Samtools release tarball,

and building the various HTSlib utilities such as bgzip is done as follows:



    cd .../samtools-1.9 # Within the unpacked release directory

    cd .../samtools-1.10 # Within the unpacked release directory

    ./configure --prefix=/path/to/location

    make all all-htslib

    make install install-htslib
@@ -48,7 +48,7 @@ There are two advantages to this: 
To build with plug-ins, you need to use the --enable-plugins configure option

as follows:



    cd .../samtools-1.9 # Within the unpacked release directory

    cd .../samtools-1.10 # Within the unpacked release directory

    ./configure --enable-plugins --prefix=/path/to/location

    make all all-htslib

    make install install-htslib
@@ -66,8 +66,8 @@ Setting --with-plugin-path is useful if you want to run directly from 
the source distribution instead of installing the package.  In that case

you can use:



    cd .../samtools-1.9 # Within the unpacked release directory

    ./configure --enable-plugins --with-plugin-path=$PWD/htslib-1.9

    cd .../samtools-1.10 # Within the unpacked release directory

    ./configure --enable-plugins --with-plugin-path=$PWD/htslib-1.10

    make all all-htslib



It is possible to override the built-in search path using the HTS_PATH