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commit 45857cd9963b212832fe2785d91403b2a5d5c65f Author: Alexandre Mestiashvili <[email protected]> Date: Thu Jul 3 21:05:53 2014 +0200 Imported Upstream version 2.0.12+dfsg --- configure | 24 ++++++++++++------------ configure.ac | 2 +- src/segment_juncs.cpp | 2 +- src/tophat-fusion-post | 2 +- src/tophat.py | 3 +++ 5 files changed, 18 insertions(+), 15 deletions(-) diff --git a/configure b/configure index 115b8dc..05fb885 100755 --- a/configure +++ b/configure @@ -1,6 +1,6 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.59 for tophat 2.0.11. +# Generated by GNU Autoconf 2.59 for tophat 2.0.12. # # Report bugs to <[email protected]>. # @@ -269,8 +269,8 @@ SHELL=${CONFIG_SHELL-/bin/sh} # Identity of this package. PACKAGE_NAME='tophat' PACKAGE_TARNAME='tophat' -PACKAGE_VERSION='2.0.11' -PACKAGE_STRING='tophat 2.0.11' +PACKAGE_VERSION='2.0.12' +PACKAGE_STRING='tophat 2.0.12' PACKAGE_BUGREPORT='[email protected]' ac_unique_file="config.h.in" @@ -792,7 +792,7 @@ if test "$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 tophat 2.0.11 to adapt to many kinds of systems. +\`configure' configures tophat 2.0.12 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -858,7 +858,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of tophat 2.0.11:";; + short | recursive ) echo "Configuration of tophat 2.0.12:";; esac cat <<\_ACEOF @@ -1009,7 +1009,7 @@ fi test -n "$ac_init_help" && exit 0 if $ac_init_version; then cat <<\_ACEOF -tophat configure 2.0.11 +tophat configure 2.0.12 generated by GNU Autoconf 2.59 Copyright (C) 2003 Free Software Foundation, Inc. @@ -1023,7 +1023,7 @@ cat >&5 <<_ACEOF This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. -It was created by tophat $as_me 2.0.11, which was +It was created by tophat $as_me 2.0.12, which was generated by GNU Autoconf 2.59. Invocation command line was $ $0 $@ @@ -1361,7 +1361,7 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu cat >>confdefs.h <<\_ACEOF -#define SVN_REVISION "4203" +#define SVN_REVISION "4238:4275M" _ACEOF @@ -1675,7 +1675,7 @@ fi # Define the identity of the package. PACKAGE='tophat' - VERSION='2.0.11' + VERSION='2.0.12' cat >>confdefs.h <<_ACEOF @@ -7134,7 +7134,7 @@ fi # Define the identity of the package. PACKAGE='tophat' - VERSION='2.0.11' + VERSION='2.0.12' cat >>confdefs.h <<_ACEOF @@ -7966,7 +7966,7 @@ _ASBOX } >&5 cat >&5 <<_CSEOF -This file was extended by tophat $as_me 2.0.11, which was +This file was extended by tophat $as_me 2.0.12, which was generated by GNU Autoconf 2.59. Invocation command line was CONFIG_FILES = $CONFIG_FILES @@ -8029,7 +8029,7 @@ _ACEOF cat >>$CONFIG_STATUS <<_ACEOF ac_cs_version="\\ -tophat config.status 2.0.11 +tophat config.status 2.0.12 configured by $0, generated by GNU Autoconf 2.59, with options \\"`echo "$ac_configure_args" | sed 's/[\\""\`\$]/\\\\&/g'`\\" diff --git a/configure.ac b/configure.ac index 936d4ec..21fb895 100644 --- a/configure.ac +++ b/configure.ac @@ -4,7 +4,7 @@ m4_include([ax_bam.m4]) #m4_include([ax_check_zlib.m4]) define([svnversion], esyscmd([sh -c "svnversion|tr -d '\n'"]))dnl -AC_INIT([tophat],[2.0.11],[[email protected]]) +AC_INIT([tophat],[2.0.12],[[email protected]]) AC_DEFINE(SVN_REVISION, "svnversion", [SVN Revision]) AC_CONFIG_SRCDIR([config.h.in]) diff --git a/src/segment_juncs.cpp b/src/segment_juncs.cpp index e3acc46..8941043 100644 --- a/src/segment_juncs.cpp +++ b/src/segment_juncs.cpp @@ -25,8 +25,8 @@ #include <bitset> #include <seqan/basic.h> #include <seqan/sequence.h> -#include <seqan/find.h> #include <seqan/file.h> +#include <seqan/find.h> #include <seqan/modifier.h> #include <seqan/align.h> #include <seqan/graph_align.h> diff --git a/src/tophat-fusion-post b/src/tophat-fusion-post index c4be6bc..c946699 100755 --- a/src/tophat-fusion-post +++ b/src/tophat-fusion-post @@ -2588,7 +2588,7 @@ def prog_path(program): def get_version(): - return "2.0.11" + return "2.0.12" def main(argv=None): diff --git a/src/tophat.py b/src/tophat.py index b4677b3..34729ed 100755 --- a/src/tophat.py +++ b/src/tophat.py @@ -1415,6 +1415,9 @@ def get_index_sam_header(params, idx_prefix, name = ""): if read_params.color: bowtie_header_cmd.append('-C') + if params.bowtie2: + bowtie_header_cmd += ["-x"] + bowtie_header_cmd.extend([idx_prefix, '/dev/null']) if noSkip: subprocess.call(bowtie_header_cmd, -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/tophat.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
