a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@378 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache
parent
32e000bbfe
commit
b4136b6d6e
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@ -127,7 +127,7 @@ public class rodSAMPileup extends ReferenceOrderedDatum implements AllelicVarian
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System.out.printf(" Exception caught during parsing Pileup line: %s%n", Utils.join(" <=> ", parts));
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throw e;
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}
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if ( nNonref > 1 ) System.out.println("SAM pileup: WARNING: multi-allelic variant at "+ loc.toString());
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if ( nNonref > 1 ) System.out.println("SAM pileup: WARNING: multi-allelic variant : ("+refBaseChar+") -->"+toMediumString());
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}
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@ -243,10 +243,13 @@ public class rodSAMPileup extends ReferenceOrderedDatum implements AllelicVarian
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}
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public String toMediumString() {
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String s = String.format("%s:%s:%s", getLocation().toString(), name, observedString);
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String s = null;
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if ( refBaseChar == '*' ) s = String.format("%s:%s:%s", getLocation().toString(), name,observedString);
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else s = String.format("%s:%s:%s/%s", getLocation().toString(), name, observedAlleles.get(0),observedAlleles.get(1));
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if ( isSNP() ) s += ": SNP";
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else {
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if ( isInsertion() ) s += ": Insertoin";
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if ( isInsertion() ) s += ": Insertion";
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else {
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if ( isDeletion() ) s+= ": Deletion";
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else {
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@ -31,7 +31,13 @@ public class MendelianInheritanceWalker extends RefWalker<TrioConcordanceRecord
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AllelicVariant dad = (rodSAMPileup)rodData.lookup("father", null);
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AllelicVariant kid = (rodSAMPileup)rodData.lookup("daughter", null);
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if ( ! hasCall(mom) || ! hasCall(dad) || ! hasCall(kid) ) return t; // at least one person is not called; nothing to do, bail out
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if ( hasCall(mom)) t.mom_assessed = 1;
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if ( hasCall(dad)) t.dad_assessed = 1;
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if ( hasCall(kid)) t.kid_assessed = 1;
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if ( hasCall(mom) && mom.isIndel() ) System.out.println("GOT INDEL: "+mom.toString());
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if (( t.mom_assessed + t.dad_assessed + t.kid_assessed) != 3 ) return t; // at least one person is not called; nothing to do, bail out
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// proceed only if we got confident calls
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@ -62,11 +68,11 @@ public class MendelianInheritanceWalker extends RefWalker<TrioConcordanceRecord
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mom_alleles.contains(kid_allele_2) && dad_alleles.contains(kid_allele_1) ) {
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t.consistent_snp = 1;
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logger.info("consistent SNP at "+context.getLocation() +
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"("+ref+") " + mom_alleles.get(0)+"/" +mom_alleles.get(1) + " " +
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dad_alleles.get(0)+"/" +dad_alleles.get(1) + " " +
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kid_allele_1+"/" +kid_allele_2
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);
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// logger.info("consistent SNP at "+context.getLocation() +
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// "("+ref+") " + mom_alleles.get(0)+"/" +mom_alleles.get(1) + " " +
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// dad_alleles.get(0)+"/" +dad_alleles.get(1) + " " +
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// kid_allele_1+"/" +kid_allele_2
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// );
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return t;
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}
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@ -27,9 +27,9 @@ public class IndelInspector extends CommandLineProgram {
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@Option(doc="Output file (sam or bam) for non-indel related reads and indel reads that were not improved") public String OUT1;
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@Option(doc="Output file (sam or bam) for improved (realigned) indel related reads") public String OUT2;
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@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;
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@Option(doc="Error counting mode: MM - count mismatches only, ERR - count errors (arachne style), MG - count mismatches and gaps as one error each") public String ERR_MODE;
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@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;
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@Option(doc="Maximum number of errors allowed (see ERR_MODE)") public Integer MAX_ERRS;
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// @Option(shortName="R", doc="Reference fasta or fasta.gz file") public File REF_FILE;
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@Option(shortName="R", doc="Reference fasta or fasta.gz file") public File REF_FILE;
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/** Required main method implementation. */
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public static void main(final String[] argv) {
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@ -38,25 +38,31 @@ public class IndelInspector extends CommandLineProgram {
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protected int doWork() {
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System.out.println("I am at version 0.3");
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int discarded_count = 0;
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ReferenceSequenceFileWalker reference = new ReferenceSequenceFileWalker(
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REF_FILE
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);
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if ( reference.getSequenceDictionary() == null ) {
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System.out.println("No reference sequence dictionary found. Abort.");
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}
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GenomeLoc.setupRefContigOrdering(reference.getSequenceDictionary());
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GenomeLoc location = null;
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if ( GENOME_LOCATION != null ) {
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location = GenomeLoc.parseGenomeLoc(GENOME_LOCATION);
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}
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if ( ! ERR_MODE.equals("MM") && ! ERR_MODE.equals("MG") && ! ERR_MODE.equals("ERR") ) {
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System.out.println("Unknown value specified for ERR_MODE");
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if ( ! ERR_MODE.equals("MM") && ! ERR_MODE.equals("MG") && ! ERR_MODE.equals("ERR") && ! ERR_MODE.equals("MC") ) {
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System.out.println("Unknown value specified for ERR_MODE: "+ERR_MODE);
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return 1;
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}
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final SAMFileReader samReader = new SAMFileReader(getInputFile(INPUT_FILE,"/broad/1KG/"));
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samReader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
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setContigOrdering(samReader);
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ReferenceSequenceFileWalker reference = new ReferenceSequenceFileWalker(
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new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")
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);
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// setContigOrdering(samReader);
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ReferenceSequence contig_seq = null;
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@ -105,7 +111,7 @@ public class IndelInspector extends CommandLineProgram {
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}
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}
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// if contig is specified and wqe did not reach it yet, skip the records until we reach that contig:
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// if contig is specified and we did not reach it yet, skip the records until we reach that contig:
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if ( location != null && GenomeLoc.compareContigs(cur_contig, location.getContig()) == -1 ) continue;
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@ -114,7 +120,22 @@ public class IndelInspector extends CommandLineProgram {
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// if stop position is specified and we are past that, stop reading:
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if ( location != null && r.getAlignmentStart() > location.getStop() ) break;
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if ( cur_contig.equals("chrM") || GenomeLoc.compareContigs(cur_contig,"chrY")==1 ) continue; // skip chrM and unplaced contigs for now
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// if ( cur_contig.equals("chrM") || GenomeLoc.compareContigs(cur_contig,"chrY") > 0 ) continue; // skip chrM and unplaced contigs for now
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// we currently do not know how to deal with cigars containing elements other than M,I,D, so
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// let's just skip the reads that contain those other elements (clipped reads?)
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Cigar c = r.getCigar();
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boolean cigar_acceptable = true;
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for ( int z = 0 ; z < c.numCigarElements() ; z++ ) {
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CigarElement ce = c.getCigarElement(z);
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switch ( ce.getOperator() ) {
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case M:
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case I:
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case D: break;
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default: cigar_acceptable = false;
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}
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}
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if ( ! cigar_acceptable ) continue;
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int err = -1;
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/*
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@ -130,12 +151,13 @@ public class IndelInspector extends CommandLineProgram {
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continue;
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*/
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if ( ERR_MODE.equals("MM")) err = numMismatches(r);
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else if ( ERR_MODE.equals("ERR")) err = numErrors(r);
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else if ( ERR_MODE.equals("MG")) err = numMismatchesGaps(r);
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if ( ERR_MODE.equals("MM")) err = numMismatches(r,contig_seq);
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else if ( ERR_MODE.equals("MC") ) err = AlignmentUtils.numMismatches(r,contig_seq);
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else if ( ERR_MODE.equals("ERR")) err = numErrors(r,contig_seq);
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else if ( ERR_MODE.equals("MG")) err = numMismatchesGaps(r,contig_seq);
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if ( err > MAX_ERRS.intValue() ) continue;
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// counter++;
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// if ( counter % 1000000 == 0 ) System.out.println(counter+" records; "+col.memStatsString());
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// counter++;
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// if ( counter % 1000000 == 0 ) System.out.println(counter+" records; "+col.memStatsString());
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col.receive(r);
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}
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@ -157,10 +179,10 @@ public class IndelInspector extends CommandLineProgram {
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* @return number of errors (number of mismatches plus total length of all insertions/deletions
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* @throws RuntimeException
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*/
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private static int numErrors(SAMRecord r) throws RuntimeException {
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private static int numErrors(SAMRecord r, ReferenceSequence refseq) throws RuntimeException {
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// NM currently stores the total number of mismatches in all blocks + 1
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int errs = numMismatches(r);
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int errs = numMismatches(r,refseq);
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// now we have to add the total length of all indels:
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Cigar c = r.getCigar();
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@ -185,10 +207,10 @@ public class IndelInspector extends CommandLineProgram {
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* deletion will be counted as a single error regardless of the length)
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* @throws RuntimeException
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*/
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private static int numMismatchesGaps(SAMRecord r) throws RuntimeException {
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private static int numMismatchesGaps(SAMRecord r,ReferenceSequence refseq) throws RuntimeException {
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// NM currently stores the total number of mismatches in all blocks + 1
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int errs = numMismatches(r);
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int errs = numMismatches(r,refseq);
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// now we have to add the total length of all indels:
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Cigar c = r.getCigar();
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@ -207,9 +229,11 @@ public class IndelInspector extends CommandLineProgram {
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}
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/** This method is a HACK: it is designed to work around the current bug in NM tags created at CRD */
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private static int numMismatches(SAMRecord r) throws RuntimeException {
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private static int numMismatches(SAMRecord r, ReferenceSequence refseq) throws RuntimeException {
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// NM currently stores the total number of mismatches in all blocks + 1
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Integer i = (Integer)r.getAttribute("NM");
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if ( i == null ) return AlignmentUtils.numMismatches(r,refseq);
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return ((Integer)r.getAttribute("NM")).intValue() - 1;
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}
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@ -265,7 +289,7 @@ public class IndelInspector extends CommandLineProgram {
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private void setDefaultContigOrdering() {
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Map<String,Integer> rco = new HashMap<String,Integer>();
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rco.put("chrM",0);
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for ( int i = 1 ; i <= 22 ; i++ ) rco.put("chr"+i,i);
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for ( int i = 1 ; i <= 22 ; i++ ) rco.put(Integer.toString(i),i);//rco.put("chr"+i,i);
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rco.put("chrX",23);
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rco.put("chrY",24);
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}
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@ -230,7 +230,7 @@ public class IndelRecordPileCollector implements RecordReceiver {
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// does nothing if alignment has no indels, otherwise adds the indels to the list and (re)sets state to 'active'
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extractIndelsAndUpdateState(r.getCigar(),currPos);
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if ( ! avoiding_region && mAllIndels.size() > 20 ) avoiding_region = true;
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if ( mState == ACTIVE_STATE && ( ! avoiding_region ) && ( mAllIndels.size() > 20 || mRecordPile.size() > 1000 ) ) avoiding_region = true;
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if ( ! avoiding_region ) mRecordPile.add(r); // add new record if this is not some crazy region
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@ -254,9 +254,11 @@ public class IndelRecordPileCollector implements RecordReceiver {
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long start = mAllIndels.first().getObject().getStart();
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long stop = mAllIndels.last().getObject().getStop();
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System.out.println("Genomic region "+mLastContig+":"+ start + "-"+ stop +
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" was ignored: "+mAllIndels.size() +" unique indels with average distance of "+
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" was ignored: ");
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System.out.println(" "+mAllIndels.size() +" unique indels with average distance of "+
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((double)(stop - start))/((double)mAllIndels.size()-1) +
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" bases between indels");
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System.out.println(" "+mRecordPile.size() +" reads collected before aborting");
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}
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// no indels or avoiding indels in bad region: send all records to defaultReceiver and clear the pile
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@ -19,6 +19,15 @@ public class TrioConcordanceRecord {
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public int inconsistent_indels_in_parent = 0 ;
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public int inconsistent_indels_in_kid = 0 ;
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public int non_biallelic = 0; // number of variant calls that are not biallelic
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public long mom_assessed = 0; // number of assessed loci for mother (i.e. passing confidence threshold filter)
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public long dad_assessed = 0;
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public long kid_assessed = 0;
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public long mom_ref = 0; // number of reference calls (out of total assessed)
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public long dad_ref = 0;
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public long kid_ref = 0;
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public long mom_snp = 0; // number of snp calls (out of total assessed)
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public long dad_snp = 0;
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public long kid_snp = 0;
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public TrioConcordanceRecord add(TrioConcordanceRecord other) {
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this.assessed_loci += other.assessed_loci;
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@ -32,6 +41,15 @@ public class TrioConcordanceRecord {
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this.inconsistent_indels_in_parent += other.inconsistent_indels_in_parent;
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this.inconsistent_indels_in_kid += other.inconsistent_indels_in_kid;
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this.non_biallelic += other.non_biallelic;
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this.mom_assessed += other.mom_assessed;
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this.dad_assessed += other.dad_assessed;
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this.kid_assessed += other.kid_assessed;
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this.mom_ref += other.mom_ref;
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this.dad_ref += other.dad_ref;
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this.kid_ref += other.kid_ref;
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this.mom_snp += other.mom_snp;
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this.dad_snp += other.dad_snp;
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this.kid_snp += other.kid_snp;
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return this;
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}
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@ -39,8 +57,11 @@ public class TrioConcordanceRecord {
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public int totalSNP() { return consistent_snp + inconsistent_snp + non_biallelic; }
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public String toString() {
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return String.format("assessed: %d; reference: %d (%3.2f); total snp: %d; consistent snp: %d (%3.2f); multiallelic: %d (%3.2f); " ,
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return String.format("%ntotal assessed in trio: %d%n reference: %d (%3.2f)%n total snp: %d%n consistent snp: %d (%3.2f)%n multiallelic: %d (%3.2f)%nper trio individual:%n assessed:%n mother: %d%n father: %d%n daughter: %d%n" ,
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assessed_loci, consistent_ref, ((double)consistent_ref*100.00)/assessed_loci,totalSNP(), consistent_snp, ((double)consistent_snp*100.0)/totalSNP(),
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non_biallelic, ((double)non_biallelic*100.0)/totalSNP());
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non_biallelic, ((double)non_biallelic*100.0)/totalSNP(),mom_assessed,dad_assessed,kid_assessed);
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// return String.format("total assessed in trio: %d%n reference: %d (%3.2f)%n total snp: %d%n consistent snp: %d (%3.2f)%n multiallelic: %d (%3.2f)" ,
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// assessed_loci, consistent_ref, ((double)consistent_ref*100.00)/assessed_loci,totalSNP(), consistent_snp, ((double)consistent_snp*100.0)/totalSNP(),
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// non_biallelic, ((double)non_biallelic*100.0)/totalSNP());
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}
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}
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