// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 26 May 2010
+// Last modified: 1 June 2010
// ---------------------------------------------------------------------------
// Prints a BAM file in the text-based SAM format.
// ***************************************************************************
#ifndef BAMTOOLS_SAM_H
#define BAMTOOLS_SAM_H
-#include <cstdlib>
-#include <iostream>
-#include <string>
-
-#include "BamReader.h"
-#include "bamtools_getopt.h"
+#include "bamtools_tool.h"
namespace BamTools {
-
-int BamSamHelp(void) {
-
- // '--head' makes more sense than '--num' from a Unix perspective, but could be confusing with header info ??
- // but this is also only the default case (from the beginning of the file)
- // do we want to add a region specifier, eg 'chr2:1000..1500'? In this case, '--num' still makes sense (give me up to N alignments from this region)
-
- std::cerr << std::endl;
- std::cerr << "usage:\tbamtools sam [--in BAM file] [--num N] [--no_header]" << std::endl;
- std::cerr << "\t-i, --in\tInput BAM file to generate SAM-format\t\t\t[default=stdin]" << std::endl;
- std::cerr << "\t-n, --num N\tOnly print up to N alignments from beginning of file\t\t[default=50*]" << endl;
- std::cerr << "\t--no_header\tOmits SAM header information from output (alignments only)\t[default=off]" << std::endl;
- std::cerr << std::endl;
- std::cerr << "* - By default bamtools sam will print all alignments in SAM format." << std::endl;
- std::cerr << " However if '-n' or '--num' is included with no N, the default of 50 is used." << std::endl;
- std::cerr << std::endl;
- return 0;
-}
-
-static RefVector references;
-
-void PrintSAM(const BamAlignment& a) {
- // tab-delimited
- // <QNAME> <FLAG> <RNAME> <POS> <MAPQ> <CIGAR> <MRNM> <MPOS> <ISIZE> <SEQ> <QUAL> [ <TAG>:<VTYPE>:<VALUE> [...] ]
+class SamTool : public AbstractTool {
- // ******************************* //
- // ** NOT FULLY IMPLEMENTED YET ** //
- //******************************** //
- //
- // Todo : build CIGAR string
- // build TAG string
- // there are some quirks, per the spec, regarding when to use '=' or not
- //
- // ******************************* //
-
- //
- // do validity check on RefID / MateRefID ??
- //
+ public:
+ SamTool(void);
+ ~SamTool(void);
- // build CIGAR string
- std::string cigarString("CIGAR:NOT YET");
+ public:
+ int Help(void);
+ int Run(int argc, char* argv[]);
+
+ private:
+ struct SamSettings;
+ SamSettings* m_settings;
+};
- // build TAG string
- std::string tagString("TAG:NOT YET");
-
- // print BamAlignment to stdout in SAM format
- std::cout << a.Name << '\t'
- << a.AlignmentFlag << '\t'
- << references[a.RefID].RefName << '\t'
- << a.Position << '\t'
- << a.MapQuality << '\t'
- << cigarString << '\t'
- << ( a.IsPaired() ? references[a.MateRefID].RefName : "*" ) << '\t'
- << ( a.IsPaired() ? a.MatePosition : 0 ) << '\t'
- << ( a.IsPaired() ? a.InsertSize : 0 ) << '\t'
- << a.QueryBases << '\t'
- << a.Qualities << '\t'
- << tagString << std::endl;
-}
-
-int RunBamSam(int argc, char* argv[]) {
-
- // else parse command line for args
- GetOpt options(argc, argv, 1);
-
- std::string inputFilename;
- options.addOption('i', "in", &inputFilename);
-
- std::string numberString;
- options.addOptionalOption('n', "num", &numberString, "50");
-
- bool isOmittingHeader;
- options.addSwitch("no_header", &isOmittingHeader);
-
- if ( !options.parse() ) return BamCoverageHelp();
- if ( inputFilename.empty() ) { inputFilename = "stdin"; }
-
- // maxNumberOfAlignments = all (if nothing specified)
- // = 50 (if '-n' or '--num' but no N)
- // = N (if '-n N' or '--num N')
- int maxNumberOfAlignments = -1;
- if ( !numberString.empty() ) { maxNumberOfAlignments = atoi(numberString.c_str()); }
-
- // open our BAM reader
- BamReader reader;
- reader.Open(inputFilename);
-
- // if header desired, retrieve and print to stdout
- if ( !isOmittingHeader ) {
- std::string header = reader.GetHeaderText();
- std::cout << header << std::endl;
- }
-
- // store reference data
- references = reader.GetReferenceData();
-
- // print all alignments to stdout in SAM format
- if ( maxNumberOfAlignments < 0 ) {
- BamAlignment ba;
- while( reader.GetNextAlignment(ba) ) {
- PrintSAM(ba);
- }
- }
-
- // print first N alignments to stdout in SAM format
- else {
- BamAlignment ba;
- int alignmentsPrinted = 0;
- while ( reader.GetNextAlignment(ba) && (alignmentsPrinted < maxNumberOfAlignments) ) {
- PrintSAM(ba);
- ++alignmentsPrinted;
- }
- }
-
- // clean & exit
- reader.Close();
- return 0;
-}
-
} // namespace BamTools
-#endif // BAMTOOLS_SAM_H
\ No newline at end of file
+#endif // BAMTOOLS_SAM_H
projects / bamtools.git / blobdiff