Added the "-list" option to all toolkit utilities that accept multiple

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

diff --git a/src/toolkit/bamtools_merge.cpp b/src/toolkit/bamtools_merge.cpp
index 2bb47c4d1846fe9ee455df317c1b0a04fdfcd51b..6a33d12352c900e3c47ac7fa61e4f53946aa9877 100644 (file)
--- a/src/toolkit/bamtools_merge.cpp
+++ b/src/toolkit/bamtools_merge.cpp
@@ -2,7 +2,7 @@
 // bamtools_merge.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 7 April 2011
+// Last modified: 10 December 2012
 // ---------------------------------------------------------------------------
 // Merges multiple BAM files into one
 // ***************************************************************************
@@ -15,6 +15,7 @@
 #include <utils/bamtools_utilities.h>
 using namespace BamTools;
 
+#include <fstream>
 #include <iostream>
 #include <string>
 #include <vector>
@@ -26,9 +27,9 @@ using namespace std;
 struct MergeTool::MergeSettings {
 
     // flags
-    bool HasInputBamFilename;
-    bool HasInputBamFilelist;
-    bool HasOutputBamFilename;
+    bool HasInput;
+    bool HasInputFilelist;
+    bool HasOutput;
     bool IsForceCompression;
     bool HasRegion;
     
@@ -42,9 +43,9 @@ struct MergeTool::MergeSettings {
     
     // constructor
     MergeSettings(void)
-        : HasInputBamFilename(false)
-       , HasInputBamFilelist(false)
-        , HasOutputBamFilename(false)
+        : HasInput(false)
+        , HasInputFilelist(false)
+        , HasOutput(false)
         , IsForceCompression(false)
         , HasRegion(false)
         , OutputFilename(Options::StandardOut())
@@ -76,20 +77,21 @@ struct MergeTool::MergeToolPrivate {
 bool MergeTool::MergeToolPrivate::Run(void) {
 
     // set to default input if none provided
-    if ( !m_settings->HasInputBamFilename && !m_settings->HasInputBamFilelist )
+    if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
         m_settings->InputFiles.push_back(Options::StandardIn());
 
     // add files in the filelist to the input file list
-    if ( m_settings->HasInputBamFilelist ) {
-       ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
-       if ( !filelist.is_open() ) {
-           cerr << "bamtools merge ERROR: could not open input BAM file list... Aborting." << endl;
-           return false;
-       }
-       string line;
-       while ( getline(filelist, line) ) {
-           m_settings->InputFiles.push_back(line);
-       }
+    if ( m_settings->HasInputFilelist ) {
+
+        ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+        if ( !filelist.is_open() ) {
+            cerr << "bamtools merge ERROR: could not open input BAM file list... Aborting." << endl;
+            return false;
+        }
+
+        string line;
+        while ( getline(filelist, line) )
+            m_settings->InputFiles.push_back(line);
     }
 
     // opens the BAM files (by default without checking for indexes)
@@ -197,13 +199,14 @@ MergeTool::MergeTool(void)
     , m_impl(0)
 {
     // set program details
-    Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one", "[ [-in <filename> -in <filename> ...] | [-list <filelist>] ] [-out <filename> | [-forceCompression]] [-region <REGION>]");
+    Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one",
+                            "[-in <filename> -in <filename> ... | -list <filelist>] [-out <filename> | [-forceCompression]] [-region <REGION>]");
     
     // 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->InputFiles,     IO_Opts);
-    Options::AddValueOption("-list",  "BAM filename", "the input BAM file list, one line per file", "", m_settings->HasInputBamFilelist,  m_settings->InputFilelist, IO_Opts);
-    Options::AddValueOption("-out", "BAM filename", "the output BAM file",   "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts);
+    Options::AddValueOption("-in",  "BAM filename", "the input BAM file(s)", "", m_settings->HasInput,  m_settings->InputFiles,     IO_Opts);
+    Options::AddValueOption("-list",  "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist,  m_settings->InputFilelist, IO_Opts);
+    Options::AddValueOption("-out", "BAM filename", "the output BAM file",   "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts);
     Options::AddOption("-forceCompression", "if results are sent to stdout (like when piping to another tool), default behavior is to leave output uncompressed. Use this flag to override and force compression", m_settings->IsForceCompression, IO_Opts);
     Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
 }