Added implementation of new SplitTool. This tool splits a single BAM file into multi...

[bamtools.git] / src / toolkit / bamtools.cpp

diff --git a/src/toolkit/bamtools.cpp b/src/toolkit/bamtools.cpp
index 20b8cf13f4db72d84bb700ccb360e3b83f993d58..39ec8427e4c017230c6b5f526f7b8a8bda822147 100644 (file)
--- a/src/toolkit/bamtools.cpp
+++ b/src/toolkit/bamtools.cpp
@@ -3,15 +3,12 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 22 July 2010
+// Last modified: 19 September 2010
 // ---------------------------------------------------------------------------
 // Integrates a number of BamTools functionalities into a single executable.
 // ***************************************************************************
 
-// Std C/C++ includes
 #include <iostream>
-
-// BamTools includes
 #include "bamtools_convert.h"
 #include "bamtools_count.h"
 #include "bamtools_coverage.h"
@@ -21,8 +18,8 @@
 #include "bamtools_merge.h"
 #include "bamtools_random.h"
 #include "bamtools_sort.h"
+#include "bamtools_split.h"
 #include "bamtools_stats.h"
-
 using namespace std;
 using namespace BamTools;
 
@@ -37,6 +34,7 @@ static const string INDEX    = "index";
 static const string MERGE    = "merge";
 static const string RANDOM   = "random";
 static const string SORT     = "sort";
+static const string SPLIT    = "split";
 static const string STATS    = "stats";
 
 // ------------------------------------------
@@ -49,6 +47,27 @@ static const string VERSION       = "version";
 static const string LONG_VERSION  = "--version";
 static const string SHORT_VERSION = "-v";
 
+// ------------------------------------------
+// Subtool factory method
+AbstractTool* CreateTool(const string& arg) {
+  
+    // determine tool type based on arg
+    if ( arg == CONVERT )  return new ConvertTool;
+    if ( arg == COUNT )    return new CountTool;
+    if ( arg == COVERAGE ) return new CoverageTool;
+    if ( arg == FILTER )   return new FilterTool;
+    if ( arg == HEADER )   return new HeaderTool;
+    if ( arg == INDEX )    return new IndexTool;
+    if ( arg == MERGE )    return new MergeTool;
+    if ( arg == RANDOM )   return new RandomTool;
+    if ( arg == SORT )     return new SortTool;
+    if ( arg == SPLIT )    return new SplitTool;
+    if ( arg == STATS )    return new StatsTool;
+
+    // unknown arg
+    return 0;
+}
+
 // ------------------------------------------
 // Print help info
 int Help(int argc, char* argv[]) {
@@ -56,17 +75,18 @@ int Help(int argc, char* argv[]) {
     // 'bamtools help COMMAND'
     if (argc > 2) {
         
-        AbstractTool* tool(0);
-        if ( argv[2] == CONVERT )  tool = new ConvertTool;
-        if ( argv[2] == COUNT )    tool = new CountTool;
-        if ( argv[2] == COVERAGE ) tool = new CoverageTool;
-        if ( argv[2] == FILTER )   tool = new FilterTool;
-        if ( argv[2] == HEADER )   tool = new HeaderTool;
-        if ( argv[2] == INDEX )    tool = new IndexTool;
-        if ( argv[2] == MERGE )    tool = new MergeTool;
-        if ( argv[2] == RANDOM )   tool = new RandomTool;
-        if ( argv[2] == SORT )     tool = new SortTool;
-        if ( argv[2] == STATS )    tool = new StatsTool;
+        AbstractTool* tool = CreateTool( argv[2] );
+//         if ( argv[2] == CONVERT )  tool = new ConvertTool;
+//         if ( argv[2] == COUNT )    tool = new CountTool;
+//         if ( argv[2] == COVERAGE ) tool = new CoverageTool;
+//         if ( argv[2] == FILTER )   tool = new FilterTool;
+//         if ( argv[2] == HEADER )   tool = new HeaderTool;
+//         if ( argv[2] == INDEX )    tool = new IndexTool;
+//         if ( argv[2] == MERGE )    tool = new MergeTool;
+//         if ( argv[2] == RANDOM )   tool = new RandomTool;
+//         if ( argv[2] == SORT )     tool = new SortTool;
+//         if ( argv[2] == SPLIT )    tool = new SplitTool;
+//         if ( argv[2] == STATS )    tool = new StatsTool;
         
         // if tool known, print its help screen
         if ( tool ) return tool->Help();
@@ -86,6 +106,7 @@ int Help(int argc, char* argv[]) {
     cerr << "\tmerge           Merge multiple BAM files into single file" << endl;
     cerr << "\trandom          Select random alignments from existing BAM file(s)" << endl;
     cerr << "\tsort            Sorts the BAM file according to some criteria" << endl;
+    cerr << "\tsplit           Splits a BAM file on user-specified property, creating a new BAM output file for each value found" << endl;
     cerr << "\tstats           Prints some basic statistics from input BAM file(s)" << endl;
     cerr << endl;
     cerr << "See 'bamtools help COMMAND' for more information on a specific command." << endl;
@@ -119,17 +140,18 @@ int main(int argc, char* argv[]) {
     if ( (argv[1] == VERSION) || (argv[1] == LONG_VERSION) || (argv[1] == SHORT_VERSION) ) return Version(); 
         
     // determine desired sub-tool
-    AbstractTool* tool(0);
-    if ( argv[1] == CONVERT )  tool = new ConvertTool;
-    if ( argv[1] == COUNT )    tool = new CountTool;
-    if ( argv[1] == COVERAGE ) tool = new CoverageTool;
-    if ( argv[1] == FILTER )   tool = new FilterTool;
-    if ( argv[1] == HEADER )   tool = new HeaderTool;
-    if ( argv[1] == INDEX )    tool = new IndexTool;
-    if ( argv[1] == MERGE )    tool = new MergeTool;
-    if ( argv[1] == RANDOM )   tool = new RandomTool;
-    if ( argv[1] == SORT )     tool = new SortTool;
-    if ( argv[1] == STATS )    tool = new StatsTool;
+    AbstractTool* tool = CreateTool( argv[1] );
+//     if ( argv[1] == CONVERT )  tool = new ConvertTool;
+//     if ( argv[1] == COUNT )    tool = new CountTool;
+//     if ( argv[1] == COVERAGE ) tool = new CoverageTool;
+//     if ( argv[1] == FILTER )   tool = new FilterTool;
+//     if ( argv[1] == HEADER )   tool = new HeaderTool;
+//     if ( argv[1] == INDEX )    tool = new IndexTool;
+//     if ( argv[1] == MERGE )    tool = new MergeTool;
+//     if ( argv[1] == RANDOM )   tool = new RandomTool;
+//     if ( argv[1] == SORT )     tool = new SortTool;
+//     if ( argv[1] == SPLIT )    tool = new SplitTool;
+//     if ( argv[1] == STATS )    tool = new StatsTool;
     
     // if found, run tool
     if ( tool ) return tool->Run(argc, argv);