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renamed standalone main 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@449 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2009-04-16 15:56:46 +00:00
parent 832afd3d60
commit e8a6cdb386
1 changed files with 0 additions and 313 deletions
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313
java/src/org/broadinstitute/sting/playground/indels/IndelInspector.java
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package org.broadinstitute.sting.playground.indels;
import java.io.File;
import java.util.List;
import java.util.Map;
import java.util.HashMap;
import javax.swing.JFileChooser;
import javax.swing.filechooser.FileNameExtensionFilter;
import edu.mit.broad.picard.cmdline.CommandLineProgram;
import edu.mit.broad.picard.cmdline.Option;
import edu.mit.broad.picard.cmdline.Usage;
import edu.mit.broad.picard.reference.ReferenceSequenceFileWalker;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.GenomeLoc;
public class IndelInspector extends CommandLineProgram {
// Usage and parameters
@Usage(programVersion="1.0") public String USAGE = "Investigates indels called in the alignment data\n";
@Option(shortName="I", doc="SAM or BAM file for calling",optional=true) public File INPUT_FILE;
@Option(shortName="L",doc="Genomic interval to run on, as contig[:start[-stop]]; whole genome if not specified", optional=true) public String GENOME_LOCATION;
@Option(shortName="V",doc="Verbosity level: SILENT, PILESUMMARY, ALIGNMENTS", optional=true) public String VERBOSITY_LEVEL;
@Option(doc="Output file (sam or bam) for non-indel related reads and indel reads that were not improved") public String OUT1;
@Option(doc="Output file (sam or bam) for improved (realigned) indel related reads") public String OUT2;
@Option(doc="[paranoid] If true, all reads that would be otherwise picked and processed by this tool will be saved, unmodified, into OUT1", optional=true) public Boolean CONTROL_RUN;
@Option(doc="Error counting mode: MM - mismatches only (from sam tags), MC - mismatches only doing actual mismatch count on the fly (use this if tags are incorrectly set); ERR - errors (arachne style: mm+gap lengths), MG - count mismatches and gaps as one error each") public String ERR_MODE;
@Option(doc="Maximum number of errors allowed (see ERR_MODE)") public Integer MAX_ERRS;
@Option(shortName="R", doc="Reference fasta or fasta.gz file") public File REF_FILE;
@Option(doc="Ignore reads that are longer than the specified cutoff (not a good way to do things but might be necessary because of performance issues)", optional=true) public Integer MAX_READ_LENGTH;
/** Required main method implementation. */
public static void main(final String[] argv) {
System.exit(new IndelInspector().instanceMain(argv));
}
protected int doWork() {
int discarded_cigar_count = 0;
int discarded_long_read_count = 0;
ReferenceSequenceFileWalker reference = new ReferenceSequenceFileWalker(
REF_FILE
);
if ( reference.getSequenceDictionary() == null ) {
System.out.println("No reference sequence dictionary found. Abort.");
}
GenomeLoc.setupRefContigOrdering(reference.getSequenceDictionary());
GenomeLoc location = null;
if ( GENOME_LOCATION != null ) {
location = GenomeLoc.parseGenomeLoc(GENOME_LOCATION);
}
if ( ! ERR_MODE.equals("MM") && ! ERR_MODE.equals("MG") && ! ERR_MODE.equals("ERR") && ! ERR_MODE.equals("MC") ) {
System.out.println("Unknown value specified for ERR_MODE: "+ERR_MODE);
return 1;
}
final SAMFileReader samReader = new SAMFileReader(getInputFile(INPUT_FILE,"/broad/1KG/"));
samReader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
// setContigOrdering(samReader);
if ( MAX_READ_LENGTH == null ) MAX_READ_LENGTH = 1000000000;
ReferenceSequence contig_seq = null;
IndelRecordPileCollector col = null;
PassThroughWriter ptWriter = new PassThroughWriter(OUT1,samReader.getFileHeader());
PileBuilder pileBuilder = null;
if ( CONTROL_RUN == null ) CONTROL_RUN=false;
if ( ! CONTROL_RUN ) pileBuilder = new PileBuilder(OUT2,samReader.getFileHeader(),ptWriter);
try {
if ( CONTROL_RUN ) col = new IndelRecordPileCollector(ptWriter, new DiscardingPileReceiver() );
else col = new IndelRecordPileCollector(ptWriter, pileBuilder );
} catch(Exception e) { System.err.println(e.getMessage()); }
if ( col == null ) return 1;
col.setControlRun(CONTROL_RUN);
if ( ! CONTROL_RUN ) {
if ( VERBOSITY_LEVEL == null ) VERBOSITY_LEVEL = new String("SILENT");
if ( VERBOSITY_LEVEL.toUpperCase().equals("SILENT")) pileBuilder.setVerbosity(PileBuilder.SILENT);
else if ( VERBOSITY_LEVEL.toUpperCase().equals("PILESUMMARY") ) pileBuilder.setVerbosity(PileBuilder.PILESUMMARY);
else if ( VERBOSITY_LEVEL.toUpperCase().equals("ALIGNMENTS") ) pileBuilder.setVerbosity(PileBuilder.ALIGNMENTS);
else {
System.out.println("Unrecognized VERBOSITY_LEVEL setting.");
return 1;
}
}
String cur_contig = null;
int counter = 0;
for ( SAMRecord r : samReader ) {
if ( r.getReadUnmappedFlag() ) continue;
if ( r.getReferenceName() != cur_contig) {
cur_contig = r.getReferenceName();
System.out.println("Contig "+cur_contig);
// if contig is specified and we are past that contig, we are done:
if ( location != null && GenomeLoc.compareContigs(cur_contig, location.getContig()) == 1 ) break;
if ( location == null || GenomeLoc.compareContigs(cur_contig, location.getContig()) == 0 ) {
contig_seq = reference.get(r.getReferenceIndex());
String refstr = new String(contig_seq.getBases());
col.setReferenceSequence(refstr);
if (!CONTROL_RUN) pileBuilder.setReferenceSequence(refstr);
System.out.println("loaded contig "+cur_contig+" (index="+r.getReferenceIndex()+"); length="+contig_seq.getBases().length+" tst="+contig_seq.toString());
}
}
// if contig is specified and we did not reach it yet, skip the records until we reach that contig:
if ( location != null && GenomeLoc.compareContigs(cur_contig, location.getContig()) == -1 ) continue;
if ( location != null && r.getAlignmentEnd() < location.getStart() ) continue;
// if stop position is specified and we are past that, stop reading:
if ( location != null && r.getAlignmentStart() > location.getStop() ) break;
// if ( cur_contig.equals("chrM") || GenomeLoc.compareContigs(cur_contig,"chrY") > 0 ) continue; // skip chrM and unplaced contigs for now
// we currently do not know how to deal with cigars containing elements other than M,I,D, so
// let's just skip the reads that contain those other elements (clipped reads?)
Cigar c = r.getCigar();
boolean cigar_acceptable = true;
for ( int z = 0 ; z < c.numCigarElements() ; z++ ) {
CigarElement ce = c.getCigarElement(z);
switch ( ce.getOperator() ) {
case M:
case I:
case D: break;
default:
cigar_acceptable = false;
}
}
if ( ! cigar_acceptable ) {
discarded_cigar_count++;
continue;
}
if ( r.getReadLength() > MAX_READ_LENGTH ) {
discarded_long_read_count++;
continue;
}
int err = -1;
/*
System.out.println("MM: "+numMismatches(r));
System.out.println("direct: "+numMismatchesDirect(r,contig_seq));
System.out.print(" ");
for ( int i = r.getAlignmentStart() - 1 ; i < r.getAlignmentEnd() ; i++ ) System.out.print((char)contig_seq.getBases()[i]);
System.out.println();
System.out.println((r.getReadNegativeStrandFlag()?"<-":"->")+r.getReadString());
System.out.println("cigar: "+r.getCigarString());
System.out.println();
if (counter++ == 20 ) break;
continue;
*/
if ( ERR_MODE.equals("MM")) err = numMismatches(r,contig_seq);
else if ( ERR_MODE.equals("MC") ) err = AlignmentUtils.numMismatches(r,contig_seq);
else if ( ERR_MODE.equals("ERR")) err = numErrors(r,contig_seq);
else if ( ERR_MODE.equals("MG")) err = numMismatchesGaps(r,contig_seq);
if ( err > MAX_ERRS.intValue() ) continue;
// counter++;
// if ( counter % 1000000 == 0 ) System.out.println(counter+" records; "+col.memStatsString());
col.receive(r);
}
if ( ! CONTROL_RUN ) {
pileBuilder.printStats();
pileBuilder.close();
}
System.out.println("done.");
System.out.println("Discarded reads with non-M,I,D cigar elements: "+ discarded_cigar_count);
System.out.println("Discarded long reads (above "+MAX_READ_LENGTH+" bp): "+ discarded_long_read_count);
System.out.println();
col.printLengthHistograms();
samReader.close();
ptWriter.close();
return 0;
}
/** This method is a HACK: it is designed to work around the current bug in NM tags created at CRD
*
* @param r SAM record that must specify an alignment
* @return number of errors (number of mismatches plus total length of all insertions/deletions
* @throws RuntimeException
*/
private static int numErrors(SAMRecord r, ReferenceSequence refseq) throws RuntimeException {
// NM currently stores the total number of mismatches in all blocks + 1
int errs = numMismatches(r,refseq);
// now we have to add the total length of all indels:
Cigar c = r.getCigar();
for ( int i = 0 ; i < c.numCigarElements() ; i++ ) {
CigarElement ce = c.getCigarElement(i);
switch( ce.getOperator()) {
case M : break; // we already have correct number of mismatches
case I :
case D :
errs += ce.getLength();
break;
default: throw new RuntimeException("Unrecognized cigar element");
}
}
return errs;
}
/** This method is a HACK: it is designed to work around the current bug in NM tags created at CRD
*
* @param r SAM record that must specify an alignment
* @return number of errors (number of mismatches plus total number of all insertions/deletions (each insertion or
* deletion will be counted as a single error regardless of the length)
* @throws RuntimeException
*/
private static int numMismatchesGaps(SAMRecord r,ReferenceSequence refseq) throws RuntimeException {
// NM currently stores the total number of mismatches in all blocks + 1
int errs = numMismatches(r,refseq);
// now we have to add the total length of all indels:
Cigar c = r.getCigar();
for ( int i = 0 ; i < c.numCigarElements() ; i++ ) {
CigarElement ce = c.getCigarElement(i);
switch( ce.getOperator()) {
case M : break; // we already have correct number of mismatches
case I :
case D :
errs++;
break;
default: throw new RuntimeException("Unrecognized cigar element");
}
}
return errs;
}
/** This method is a HACK: it is designed to work around the current bug in NM tags created at CRD */
private static int numMismatches(SAMRecord r, ReferenceSequence refseq) throws RuntimeException {
// NM currently stores the total number of mismatches in all blocks + 1
Integer i = (Integer)r.getAttribute("NM");
if ( i == null ) return AlignmentUtils.numMismatches(r,refseq);
return ((Integer)r.getAttribute("NM")).intValue() - 1;
}
/** Trivial utility method that goes some distance trying to ensure that the input file is there;
* the only purpose is reducing clutter in main(). Receives a default
* input file argument, does a few checks (e.g. that it is non-null and exists), if they fail tries
* to fire up a file chooser dialog using start_folder as initial directory, etc.
* @param default_arg some "default" input file; if it is non-null and exists, nothing else will be done,
* and the same default_arg objetc will be returned; otherwise the method will try to ask for a "better" input.
* @param start_folder should file open dialog be fired up, it will initially display this directory.
* @return File object that is not null and does exist (there is no check that it is a valid SAM/BAM file though).
*/
private File getInputFile(File default_arg, String start_folder) {
File f = default_arg;
if ( f==null || ! f.exists() ) {
JFileChooser fc = new JFileChooser(start_folder);
FileNameExtensionFilter ff = new FileNameExtensionFilter("SAM and BAM files","sam","bam");
fc.setFileFilter(ff);
fc.setFileSelectionMode(JFileChooser.FILES_ONLY);
int ret = fc.showOpenDialog(null);
f = fc.getSelectedFile();
if ( ret != JFileChooser.APPROVE_OPTION ) {
System.out.println("No input file specified. Exiting...");
System.exit(1);
}
}
if ( f == null || ! f.exists() ) {
System.out.println("SAM or BAM input file must be specified. Exiting...");
System.exit(1);
}
return f;
}
/** Auxiliary method to remove some clutter from main(); gets called only once and tries to get
* contig ordering from the header provided by opened SAM reader; if no header info is available
* falls back to default ordering; whichever ordering is used, it is set for GenomeLoc class.
* @param r sam reader to get header from
*/
private void setContigOrdering(SAMFileReader r) {
SAMFileHeader h = r.getFileHeader();
if ( h == null ) {
System.out.println("No header found in SAM file, falling back to default contig ordering");
setDefaultContigOrdering();
return;
}
GenomeLoc.setupRefContigOrdering(h.getSequenceDictionary());
}
private void setDefaultContigOrdering() {
Map<String,Integer> rco = new HashMap<String,Integer>();
rco.put("chrM",0);
for ( int i = 1 ; i <= 22 ; i++ ) rco.put(Integer.toString(i),i);//rco.put("chr"+i,i);
rco.put("chrX",23);
rco.put("chrY",24);
}
}