From e8a6cdb386fbc8ef464820cef9de61cd6e631e85 Mon Sep 17 00:00:00 2001 From: asivache Date: Thu, 16 Apr 2009 15:56:46 +0000 Subject: [PATCH] renamed standalone main git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@449 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/indels/IndelInspector.java | 313 ------------------ 1 file changed, 313 deletions(-) delete mode 100755 java/src/org/broadinstitute/sting/playground/indels/IndelInspector.java diff --git a/java/src/org/broadinstitute/sting/playground/indels/IndelInspector.java b/java/src/org/broadinstitute/sting/playground/indels/IndelInspector.java deleted file mode 100755 index 8070c3e26..000000000 --- a/java/src/org/broadinstitute/sting/playground/indels/IndelInspector.java +++ /dev/null @@ -1,313 +0,0 @@ -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 rco = new HashMap(); - 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); - } -}