1 // ***************************************************************************
2 // bamtools_coverage.h (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 26 May 2010
7 // ---------------------------------------------------------------------------
8 // Prints coverage statistics for a single BAM file
10 // ** Expand to multiple??
12 // ***************************************************************************
14 #ifndef BAMTOOLS_COVERAGE_H
15 #define BAMTOOLS_COVERAGE_H
20 #include "BamReader.h"
21 #include "bamtools_getopt.h"
25 int BamCoverageHelp(void) {
26 std::cerr << std::endl;
27 std::cerr << "usage:\tbamtools coverage [--in BAM file]" << std::endl;
28 std::cerr << "\t-i, --in\tInput BAM file to generate coverage stats\t[default=stdin]" << std::endl;
29 std::cerr << std::endl;
33 int RunBamCoverage(int argc, char* argv[]) {
35 // else parse command line for args
36 GetOpt options(argc, argv, 1);
38 std::string inputFilename;
39 options.addOption('i', "in", &inputFilename);
41 if ( !options.parse() ) return BamCoverageHelp();
42 if ( inputFilename.empty() ) { inputFilename = "stdin"; }
44 // // open our BAM reader
46 // reader.Open(inputFilename);
48 // generate coverage stats
49 std::cerr << "Generating coverage stats for " << inputFilename << std::endl;
50 std::cerr << "FEATURE NOT YET IMPLEMENTED!" << std::endl;
57 } // namespace BamTools
59 #endif // BAMTOOLS_COVERAGE_H