From: Erik Garrison <erik.garrison@bc.edu>
Date: Wed, 7 Jul 2010 19:54:39 +0000 (-0400)
Subject: Merge BamMultiReader and SetRegion into bamtools convert
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=155ba46a7dc23b749cc353b194f7ae6336f9f23d;p=bamtools.git

Merge BamMultiReader and SetRegion into bamtools convert

This commit merges the BamMultiReader and SetRegion method into the
conversion tool.  This greatly simplifies the process of dumping
alignments from regions in a set of bam files.

Breaking in this commit: stdin input by default.  To be fixed in a
subsequent commit.
---

diff --git a/bamtools_convert.cpp b/bamtools_convert.cpp
index 655c25a..633c21d 100644
--- a/bamtools_convert.cpp
+++ b/bamtools_convert.cpp
@@ -16,6 +16,7 @@
 #include "bamtools_convert.h"
 //#include "bamtools_format.h"
 #include "bamtools_options.h"
+#include "bamtools_utilities.h"
 #include "BGZF.h"
 #include "BamReader.h"
 #include "BamMultiReader.h"
@@ -45,20 +46,25 @@ namespace BamTools {
 struct ConvertTool::ConvertSettings {
 
     // flags
-    bool HasInputBamFilename;
+    bool HasInputBamFilenames;
     bool HasOutputBamFilename;
     bool HasFormat;
+    bool HasRegion;
 
     // filenames
-    string InputFilename;
+    //string InputFilename;
+    vector<string> InputFiles;
     string OutputFilename;
     string Format;
+
+    // region
+    string Region;
     
     // constructor
     ConvertSettings(void)
-        : HasInputBamFilename(false)
+        : HasInputBamFilenames(false)
         , HasOutputBamFilename(false)
-        , InputFilename(Options::StandardIn())
+        //, InputFilename(Options::StandardIn())
         , OutputFilename(Options::StandardOut())
     { } 
 };  
@@ -75,9 +81,12 @@ ConvertTool::ConvertTool(void)
     
     // set up options 
     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
-    Options::AddValueOption("-in",     "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename,  m_settings->InputFilename,  IO_Opts, Options::StandardIn());
+    //Options::AddValueOption("-in",     "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename,  m_settings->InputFilename,  IO_Opts, Options::StandardIn());
+    Options::AddValueOption("-in",  "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilenames,  m_settings->InputFiles, IO_Opts, Options::StandardIn());
     Options::AddValueOption("-out",    "BAM filename", "the output BAM file",   "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
     Options::AddValueOption("-format", "FORMAT", "the output file format - see README for recognized formats", "", m_settings->HasFormat, m_settings->Format, IO_Opts);
+    OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
+    Options::AddValueOption("-region", "REGION", "genomic region. Index file is recommended for better performance, and is read automatically if it exists as <filename>.bai. See \'bamtools help index\' for more  details on creating one", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
 }
 
 ConvertTool::~ConvertTool(void) {
@@ -98,9 +107,16 @@ int ConvertTool::Run(int argc, char* argv[]) {
     Options::Parse(argc, argv, 1);
     
     // open files
-    BamReader reader;
-    reader.Open(m_settings->InputFilename);
+    BamMultiReader reader;
+    reader.Open(m_settings->InputFiles);
     references = reader.GetReferenceData();
+
+    BamRegion region;
+    if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
+        if ( !reader.SetRegion(region) ) {
+           cerr << "Could not set BamReader region to REGION: " << m_settings->Region << endl;
+        }
+    }
         
     // ----------------------------------------
     // do conversion,depending on desired output format