New upstream version 1.10.1 (581cbb1d) · Commits · Debian Med / htslib

Makefile

+2 −0

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		@@ -30,6 +30,8 @@ RANLIB = ranlib
		htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl

		CPPFLAGS =
		# TODO: make the 64-bit support for VCF optional via configure, for now add -DVCF_ALLOW_INT64
		# to CFLAGS manually, here or in config.mk if the latter exists.
		# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
		# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
		#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600

NEWS

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		Noteworthy changes in release a.b
		~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

		Noteworthy changes in release 1.10.1 (17th December 2019)
		~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

		The support for 64-bit coordinates in VCF brought problems for files
		not conforming to VCF/BCF specification. While previous versions would
		make out-of-range values silently overflow creating nonsense values
		but parseable file, the version 1.10 would silently create an invalid BCF.


		Noteworthy changes in release 1.10 (6th December 2019)
		~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

README.large_positions.md

+3 −1

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		@@ -9,7 +9,9 @@ which have, or are expected to have, chromosomes longer than two gigabases.
		Currently 64 bit positions can only be stored in SAM and VCF format files.
		Binary BAM, CRAM and BCF cannot be used due to limitations in the formats
		themselves. As SAM and VCF are text formats, they have no limit on the
		size of numeric values.
		size of numeric values. Note that while 64 bit positions are supported by
		default for SAM, for VCF they must be enabled explicitly at compile time
		by editing Makefile and adding -DVCF_ALLOW_INT64=1 to CFLAGS.

		# Compatibility issues to check

configure

+9 −9

Original line number	Diff line number	Diff line
		#! /bin/sh
		# Guess values for system-dependent variables and create Makefiles.
		# Generated by GNU Autoconf 2.68 for HTSlib 1.10.
		# Generated by GNU Autoconf 2.68 for HTSlib 1.10.1.
		#
		# Report bugs to <samtools-help@lists.sourceforge.net>.
		#
		@@ -565,8 +565,8 @@ MAKEFLAGS=
		# Identity of this package.
		PACKAGE_NAME='HTSlib'
		PACKAGE_TARNAME='htslib'
		PACKAGE_VERSION='1.10'
		PACKAGE_STRING='HTSlib 1.10'
		PACKAGE_VERSION='1.10.1'
		PACKAGE_STRING='HTSlib 1.10.1'
		PACKAGE_BUGREPORT='samtools-help@lists.sourceforge.net'
		PACKAGE_URL='http://www.htslib.org/'

		@@ -1245,7 +1245,7 @@ if test "$ac_init_help" = "long"; then
		# Omit some internal or obsolete options to make the list less imposing.
		# This message is too long to be a string in the A/UX 3.1 sh.
		cat <<_ACEOF
		\`configure' configures HTSlib 1.10 to adapt to many kinds of systems.
		\`configure' configures HTSlib 1.10.1 to adapt to many kinds of systems.

		Usage: $0 [OPTION]... [VAR=VALUE]...

		@@ -1306,7 +1306,7 @@ fi

		if test -n "$ac_init_help"; then
		case $ac_init_help in
		short \| recursive ) echo "Configuration of HTSlib 1.10:";;
		short \| recursive ) echo "Configuration of HTSlib 1.10.1:";;
		esac
		cat <<\_ACEOF

		@@ -1413,7 +1413,7 @@ fi
		test -n "$ac_init_help" && exit $ac_status
		if $ac_init_version; then
		cat <<\_ACEOF
		HTSlib configure 1.10
		HTSlib configure 1.10.1
		generated by GNU Autoconf 2.68

		Copyright (C) 2010 Free Software Foundation, Inc.
		@@ -1742,7 +1742,7 @@ cat >config.log <<_ACEOF
		This file contains any messages produced by compilers while
		running configure, to aid debugging if configure makes a mistake.

		It was created by HTSlib $as_me 1.10, which was
		It was created by HTSlib $as_me 1.10.1, which was
		generated by GNU Autoconf 2.68. Invocation command line was

		$ $0 $@
		@@ -5804,7 +5804,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF \|\| ac_write_fail=1
		# report actual input values of CONFIG_FILES etc. instead of their
		# values after options handling.
		ac_log="
		This file was extended by HTSlib $as_me 1.10, which was
		This file was extended by HTSlib $as_me 1.10.1, which was
		generated by GNU Autoconf 2.68. Invocation command line was

		CONFIG_FILES = $CONFIG_FILES
		@@ -5867,7 +5867,7 @@ _ACEOF
		cat >>$CONFIG_STATUS <<_ACEOF \|\| ac_write_fail=1
		ac_cs_config="`$as_echo "$ac_configure_args" \| sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
		ac_cs_version="\\
		HTSlib config.status 1.10
		HTSlib config.status 1.10.1
		configured by $0, generated by GNU Autoconf 2.68,
		with options \\"\$ac_cs_config\\"

htslib/hts.h

+1 −1

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		@@ -421,7 +421,7 @@ const char *hts_version(void);
		// Immediately after release, bump ZZ to 90 to distinguish in-development
		// Git repository builds from the release; you may wish to increment this
		// further when significant features are merged.
		#define HTS_VERSION 101000
		#define HTS_VERSION 101001

		/*!
		@abstract Determine format by peeking at the start of a file