biology/samtools: Upgrade to 1.11
Numerous new features, bug fixes and performance enhancements https://github.com/samtools/samtools/releases/tag/1.11 Reported by: portscout
This commit is contained in:
Jason W. Bacon
parent
6fd02632f0
commit
025ca27d46
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=554156
@ -2,7 +2,7 @@
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# $FreeBSD$
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PORTNAME= samtools
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DISTVERSION= 1.10
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DISTVERSION= 1.11
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CATEGORIES= biology
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MAINTAINER= jwb@FreeBSD.org
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@ -20,7 +20,6 @@ USE_GITHUB= yes
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USE_PERL5= test
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GNU_CONFIGURE= yes
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SUB_FILES= pkg-message
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SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl
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TEST_TARGET= test
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@ -1,3 +1,3 @@
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TIMESTAMP = 1595117115
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SHA256 (samtools-samtools-1.10_GH0.tar.gz) = 382843e85fdb55868cebaaf2585c43776762d099581341b5803677de5ed117a9
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SIZE (samtools-samtools-1.10_GH0.tar.gz) = 4457760
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TIMESTAMP = 1602982679
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SHA256 (samtools-samtools-1.11_GH0.tar.gz) = 80a54e93c5d111c15c005ee96a578bcd7e1bde34dba2242d981c539ff32f1738
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SIZE (samtools-samtools-1.11_GH0.tar.gz) = 4516328
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@ -1,25 +1,7 @@
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--- Makefile.orig 2019-12-06 16:40:42 UTC
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--- Makefile.orig 2020-10-18 00:55:50 UTC
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+++ Makefile
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@@ -21,12 +21,12 @@
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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# DEALINGS IN THE SOFTWARE.
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-CC = gcc
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-AR = ar
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-CPPFLAGS =
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+CC ?= gcc
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+AR ?= ar
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+# CPPFLAGS =
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#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
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-CFLAGS = -g -Wall -O2
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-LDFLAGS =
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+CFLAGS ?= -g -Wall -O2
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+# LDFLAGS =
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LIBS =
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LZ4DIR = ./lz4
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@@ -47,23 +47,24 @@ AOBJS= bam_index.o bam_plcmd.o sam_view.o bam_fas
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bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o
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@@ -49,7 +49,8 @@ AOBJS= bam_index.o bam_plcmd.o sam_view.o bam_fas
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bam_ampliconclip.o amplicon_stats.o
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LZ4OBJS = $(LZ4DIR)/lz4.o
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-prefix = /usr/local
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@ -28,27 +10,26 @@
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exec_prefix = $(prefix)
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bindir = $(exec_prefix)/bin
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datarootdir = $(prefix)/share
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-mandir = $(datarootdir)/man
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+mandir = $(prefix)/man
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man1dir = $(mandir)/man1
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@@ -59,14 +60,14 @@ man1dir = $(mandir)/man1
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# Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
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-misc_bindir = $(bindir)
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+misc_bindir = $(bindir)/samtools_misc
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misc_bindir = $(bindir)
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+# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
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MKDIR_P = mkdir -p
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-MKDIR_P = mkdir -p
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-INSTALL = install -p
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-INSTALL_DATA = $(INSTALL) -m 644
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-INSTALL_DIR = $(MKDIR_P) -m 755
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-INSTALL_MAN = $(INSTALL_DATA)
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-INSTALL_PROGRAM = $(INSTALL)
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-INSTALL_SCRIPT = $(INSTALL_PROGRAM)
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-
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+# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set
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+MKDIR_P = mkdir -p
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+INSTALL = install -p
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+INSTALL_DATA = ${BSD_INSTALL_DATA}
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+INSTALL_DIR = $(MKDIR_P)
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+INSTALL_MAN = ${BSD_INSTALL_MAN}
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+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
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+INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT}
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PROGRAMS = samtools
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@ -1,13 +0,0 @@
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[
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{ type: install
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message: <<EOM
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The miscellaneous tools included with Samtools have been installed to
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%%PREFIX%%/bin/samtools_misc
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Add that directory to your path if you want to use these tools.
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Some of these tools depend on Perl5/Python, and it will need to be installed to
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use them.
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EOM
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}
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]
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@ -1,28 +1,32 @@
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bin/ace2sam
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bin/blast2sam.pl
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bin/bowtie2sam.pl
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bin/export2sam.pl
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bin/interpolate_sam.pl
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bin/maq2sam-long
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bin/maq2sam-short
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bin/md5fa
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bin/md5sum-lite
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bin/novo2sam.pl
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bin/plot-ampliconstats
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bin/plot-bamstats
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bin/psl2sam.pl
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bin/sam2vcf.pl
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bin/samtools
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bin/samtools_misc/ace2sam
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bin/samtools_misc/blast2sam.pl
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bin/samtools_misc/bowtie2sam.pl
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bin/samtools_misc/export2sam.pl
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bin/samtools_misc/interpolate_sam.pl
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bin/samtools_misc/maq2sam-long
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bin/samtools_misc/maq2sam-short
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bin/samtools_misc/md5fa
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bin/samtools_misc/md5sum-lite
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bin/samtools_misc/novo2sam.pl
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bin/samtools_misc/plot-bamstats
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bin/samtools_misc/psl2sam.pl
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bin/samtools_misc/sam2vcf.pl
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bin/samtools_misc/samtools.pl
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bin/samtools_misc/seq_cache_populate.pl
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bin/samtools_misc/soap2sam.pl
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bin/samtools_misc/wgsim
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bin/samtools_misc/wgsim_eval.pl
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bin/samtools_misc/zoom2sam.pl
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bin/samtools.pl
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bin/seq_cache_populate.pl
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bin/soap2sam.pl
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bin/wgsim
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bin/wgsim_eval.pl
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bin/zoom2sam.pl
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man/man1/samtools-addreplacerg.1.gz
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man/man1/samtools-ampliconclip.1.gz
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man/man1/samtools-ampliconstats.1.gz
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man/man1/samtools-bedcov.1.gz
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man/man1/samtools-calmd.1.gz
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man/man1/samtools-cat.1.gz
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man/man1/samtools-collate.1.gz
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man/man1/samtools-coverage.1.gz
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man/man1/samtools-depad.1.gz
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man/man1/samtools-depth.1.gz
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man/man1/samtools-dict.1.gz
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