patch samtools to handle situation where LB tags aren't in the @RG he…

…ader line

README.textile

@@ -84,12 +84,12 @@ h2. Build Dependencies
 h3. Available Packages for Dependencies
 * For APT-based systems (Debian, Ubuntu), install the following packages:
 
-bc. sudo apt-get install build-essential git-core cmake zlib1g-dev libncurses-dev
+bc. sudo apt-get install build-essential git-core cmake zlib1g-dev libncurses-dev patch
 
 * For RPM-based systems (Fedora, CentOS, RHEL), install the following packages instead:
 
 bc. sudo yum groupinstall "Development tools" 
-sudo yum install zlib-devel ncurses-devel cmake
+sudo yum install zlib-devel ncurses-devel cmake patch
 
 Note that for some RPM based systems (like RHEL), you will need to install cmake 2.8 or greater yourself as the packaged version is much older.
 
@@ -104,7 +104,7 @@ bc.         git clone https://github.com/genome/bam-readcount.git
 h3. Compile bam-readcount
 * bam-readcount does not support in source builds. Create a new build directory, enter it, and run:
 
-bc..         cmake /path/to/bam-readcount/repo
+bc.         cmake /path/to/bam-readcount/repo
         make deps
         make
 

cmake/BuildSamtools.cmake

@@ -31,6 +31,7 @@ ExternalProject_Add(
     URL ${CMAKE_SOURCE_DIR}/vendor/samtools-0.1.19.tar.gz
     SOURCE_DIR ${SAMTOOLS_ROOT}
     BINARY_DIR ${SAMTOOLS_ROOT}
+    PATCH_COMMAND patch -p2 -t -N < ${CMAKE_SOURCE_DIR}/vendor/samtools0.1.19.patch
     CONFIGURE_COMMAND echo "Building samtools, build log at ${SAMTOOLS_LOG}"
     BUILD_COMMAND make INCLUDES=-I${ZLIB_INCLUDE_DIRS} libbam.a > ${SAMTOOLS_LOG} 2>&1
     INSTALL_COMMAND ""

vendor/samtools0.1.19.patch

@@ -0,0 +1,11 @@
+--- samtools-0.1.19/sam_header.c	2013-03-19 02:48:09.000000000 -0500
++++ vendor/samtools/sam_header.c	2014-04-23 20:58:22.114860000 -0500
+@@ -687,7 +687,7 @@
+         HeaderTag *key, *value;
+         key   = header_line_has_tag(hline,key_tag);
+         value = header_line_has_tag(hline,value_tag);
+-        if ( !key && !value ) 
++        if ( !key || !value ) 
+         {
+             l = l->next;
+             continue;