[med-svn] [tophat] 01/07: Imported Upstream version 2.0.12+dfsg

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository tophat.

commit 45857cd9963b212832fe2785d91403b2a5d5c65f
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
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 <tophat.cufflinks at gmail.com>.
 #
@@ -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='tophat.cufflinks at gmail.com'
 
 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],[tophat.cufflinks at gmail.com])
+AC_INIT([tophat],[2.0.12],[tophat.cufflinks at gmail.com])
 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,

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