bamtools.cpp

   1 // ***************************************************************************
   2 // bamtools.cpp (c) 2010 Erik Garrison
   3 // Marth Lab, Department of Biology, Boston College
   4 // All rights reserved.
   5 // ---------------------------------------------------------------------------
   6 // Integrates a number of BamTools functionalities into a single executable.
   7 // ***************************************************************************
   8
   9 // Std C/C++ includes
  10 #include <cstdlib>
  11 #include <iostream>
  12 #include <string>
  13 #include <boost/algorithm/string.hpp>
  14 using namespace std;
  15
  16 // BamTools includes
  17 #include "BamReader.h"
  18 #include "BamWriter.h"
  19 #include "BamMultiReader.h"
  20 using namespace BamTools;
  21
  22 void usageSummary() {
  23     cerr << "usage: bamtools <command> [options]" << endl
  24          << "actions:" << endl
  25          << "    index <bam file>" << endl
  26          << "    merge <merged BAM file> [<BAM file> <BAM file> ...]" << endl
  27          << "    dump [<BAM file> <BAM file> ...]" << endl;
  28          //<< "    trim <input BAM file> <input BAM index file> <output BAM file> <reference name> <leftBound> <rightBound>" << endl;
  29 }
  30
  31
  32 void BamMerge(string outputFilename, vector<string> filenames) {
  33
  34     BamMultiReader reader;
  35
  36     reader.Open(filenames);
  37
  38     string mergedHeader = reader.GetHeaderText();
  39
  40     RefVector references = reader.GetReferenceData();
  41
  42     // open BamWriter
  43     BamWriter writer;
  44     writer.Open( outputFilename.c_str(), mergedHeader, references);
  45
  46     BamAlignment bAlignment;
  47     while (reader.GetNextAlignment(bAlignment)) {
  48         // write to output file
  49         writer.SaveAlignment(bAlignment);
  50     }
  51
  52     // close output file
  53     writer.Close();
  54     // close input files
  55     reader.Close();
  56
  57 }
  58
  59 void BamCreateIndex(const char* inputFilename) {
  60
  61         // open our BAM reader
  62         BamReader reader;
  63         reader.Open(inputFilename);
  64
  65     // create index file
  66     reader.CreateIndex();
  67
  68         // close our file
  69         reader.Close();
  70
  71 }
  72
  73 // Spit out basic BamAlignment data
  74 void PrintAlignment(const BamAlignment& alignment) {
  75         cout << "---------------------------------" << endl;
  76         cout << "Name: "       << alignment.Name << endl;
  77         cout << "Aligned to: " << alignment.RefID;
  78         cout << ":"            << alignment.Position << endl;
  79         cout << endl;
  80 }
  81
  82 void BamDump(vector<string> files) {
  83
  84         BamMultiReader reader;
  85         reader.Open(files);
  86
  87         BamAlignment bAlignment;
  88         while (reader.GetNextAlignment(bAlignment)) {
  89             PrintAlignment(bAlignment);
  90         }
  91
  92         reader.Close();
  93
  94 }
  95
  96
  97 int main(int argc, char* argv[]) {
  98
  99         // validate argument count
 100         if( argc < 2 ) {
 101         usageSummary();
 102                 exit(1);
 103         }
 104
 105     string command = argv[1];
 106
 107     if (command == "index") {
 108         BamCreateIndex(argv[2]);
 109     } else if (command == "merge") {
 110         vector<string> files;
 111         string outputFile = argv[2];
 112         for (int i = 3; i<argc; ++i) {
 113             files.push_back(argv[i]);
 114         }
 115         BamMerge(outputFile, files);
 116     } else if (command == "dump") {
 117         vector<string> files;
 118         for (int i = 2; i<argc; ++i) {
 119             files.push_back(argv[i]);
 120         }
 121         BamDump(files);
 122     }
 123
 124
 125         return 0;
 126 }