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

java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java

@@ -127,7 +127,7 @@ public class rodSAMPileup extends ReferenceOrderedDatum implements AllelicVarian
             System.out.printf("  Exception caught during parsing Pileup line:  %s%n", Utils.join(" <=> ", parts));
             throw e;
         }
-        if ( nNonref > 1 ) System.out.println("SAM pileup: WARNING: multi-allelic variant at "+ loc.toString());
+        if ( nNonref > 1 ) System.out.println("SAM pileup: WARNING: multi-allelic variant :  ("+refBaseChar+") -->"+toMediumString());
     }
 
     
@@ -243,10 +243,13 @@ public class rodSAMPileup extends ReferenceOrderedDatum implements AllelicVarian
     }
 
     public String toMediumString() {
-        String s = String.format("%s:%s:%s", getLocation().toString(), name, observedString);
+    	
+        String s = null;
+        if ( refBaseChar == '*' ) s = String.format("%s:%s:%s", getLocation().toString(), name,observedString);
+        else s = String.format("%s:%s:%s/%s", getLocation().toString(), name, observedAlleles.get(0),observedAlleles.get(1));
         if ( isSNP() ) s += ": SNP";
         else {
-        	if ( isInsertion() ) s += ": Insertoin";
+        	if ( isInsertion() ) s += ": Insertion";
         	else {
         		if ( isDeletion() ) s+= ": Deletion";
         		else {

java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java

@@ -31,7 +31,13 @@ public class MendelianInheritanceWalker  extends RefWalker<TrioConcordanceRecord
 		AllelicVariant dad = (rodSAMPileup)rodData.lookup("father", null);
 		AllelicVariant kid = (rodSAMPileup)rodData.lookup("daughter", null);
 		
-		if ( ! hasCall(mom)  || ! hasCall(dad) || ! hasCall(kid) ) return t; // at least one person is not called; nothing to do, bail out
+		if ( hasCall(mom)) t.mom_assessed = 1;
+		if ( hasCall(dad)) t.dad_assessed = 1;
+		if ( hasCall(kid)) t.kid_assessed = 1;
+		
+		if ( hasCall(mom) && mom.isIndel() ) System.out.println("GOT INDEL: "+mom.toString());
+		
+		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
 			
 		// proceed only if we got confident calls
 			
@@ -62,11 +68,11 @@ public class MendelianInheritanceWalker  extends RefWalker<TrioConcordanceRecord
 				mom_alleles.contains(kid_allele_2) && dad_alleles.contains(kid_allele_1) ) {
 			t.consistent_snp = 1;
 			
-			logger.info("consistent SNP at "+context.getLocation() + 
+//			logger.info("consistent SNP at "+context.getLocation() + 
-					"("+ref+") " + mom_alleles.get(0)+"/" +mom_alleles.get(1) + "  " +
+//					"("+ref+") " + mom_alleles.get(0)+"/" +mom_alleles.get(1) + "  " +
-					dad_alleles.get(0)+"/" +dad_alleles.get(1) + "  " +
+//					dad_alleles.get(0)+"/" +dad_alleles.get(1) + "  " +
-					kid_allele_1+"/" +kid_allele_2  
+//					kid_allele_1+"/" +kid_allele_2  
-					);
+//					);
 			return t;
 	    }
 		

java/src/org/broadinstitute/sting/playground/indels/IndelInspector.java

@@ -27,9 +27,9 @@ public class IndelInspector extends CommandLineProgram {
     @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 - count mismatches only, ERR - count errors (arachne style), MG - count mismatches and gaps as one error each") public String ERR_MODE;
+    @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(shortName="R", doc="Reference fasta or fasta.gz file") public File REF_FILE;
 
     /** Required main method implementation. */
     public static void main(final String[] argv) {
@@ -38,25 +38,31 @@ public class IndelInspector extends CommandLineProgram {
     
     protected int doWork() {
 
-        System.out.println("I am at version 0.3");
+        int discarded_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") ) {
+        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");
+            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);
+        //        setContigOrdering(samReader);
-
-        ReferenceSequenceFileWalker reference = new ReferenceSequenceFileWalker(
-                    new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")
-            );
 
 
         ReferenceSequence contig_seq = null;
@@ -105,7 +111,7 @@ public class IndelInspector extends CommandLineProgram {
                 }
             }
 
-            // if contig is specified and wqe did not reach it yet, skip the records until we reach that contig:
+            // 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;
 
 
@@ -114,7 +120,22 @@ public class IndelInspector extends CommandLineProgram {
             // 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")==1 ) continue; // skip chrM and unplaced contigs for now
+            //    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 ) continue;
 
             int err = -1;
 /*
@@ -130,12 +151,13 @@ public class IndelInspector extends CommandLineProgram {
             continue;
 */
 
-        	if ( ERR_MODE.equals("MM")) err = numMismatches(r);
+            if ( ERR_MODE.equals("MM")) err = numMismatches(r,contig_seq);
-        	else if ( ERR_MODE.equals("ERR")) err = numErrors(r);
+            else if ( ERR_MODE.equals("MC") ) err = AlignmentUtils.numMismatches(r,contig_seq);
-        	else if ( ERR_MODE.equals("MG")) err = numMismatchesGaps(r);
+            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++;
+            //        	counter++;
-//        	if ( counter % 1000000 == 0 ) System.out.println(counter+" records; "+col.memStatsString());
+            //        	if ( counter % 1000000 == 0 ) System.out.println(counter+" records; "+col.memStatsString());
             col.receive(r);
 
         }
@@ -157,10 +179,10 @@ public class IndelInspector extends CommandLineProgram {
 	 * @return number of errors (number of mismatches plus total length of all insertions/deletions
 	 * @throws RuntimeException
 	 */
-	private static int numErrors(SAMRecord r) 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);
+        int errs = numMismatches(r,refseq);
 		
 		// now we have to add the total length of all indels:
 		Cigar c = r.getCigar();
@@ -185,10 +207,10 @@ public class IndelInspector extends CommandLineProgram {
 	 * deletion will be counted as a single error regardless of the length)
 	 * @throws RuntimeException
 	 */
-	private static int numMismatchesGaps(SAMRecord r) 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);
+        int errs = numMismatches(r,refseq);
 		
 		// now we have to add the total length of all indels:
 		Cigar c = r.getCigar();
@@ -207,9 +229,11 @@ public class IndelInspector extends CommandLineProgram {
 	}
 
     /** 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) throws RuntimeException {
+    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;
 		
     }
@@ -265,7 +289,7 @@ public class IndelInspector extends CommandLineProgram {
     private void setDefaultContigOrdering() {
         Map<String,Integer> rco = new HashMap<String,Integer>();
         rco.put("chrM",0);
-        for ( int i = 1 ; i <= 22 ; i++ ) rco.put("chr"+i,i);
+        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);
     }

java/src/org/broadinstitute/sting/playground/indels/IndelRecordPileCollector.java

@@ -230,7 +230,7 @@ public class IndelRecordPileCollector implements RecordReceiver {
         // does nothing if alignment has no indels, otherwise adds the indels to the list and (re)sets state to 'active'
         extractIndelsAndUpdateState(r.getCigar(),currPos);
 
-		if ( ! avoiding_region && mAllIndels.size() > 20 ) avoiding_region = true;
+        if ( mState == ACTIVE_STATE && ( ! avoiding_region ) && ( mAllIndels.size() > 20 || mRecordPile.size() > 1000 ) ) avoiding_region = true;
 
         if ( ! avoiding_region ) mRecordPile.add(r); // add new record if this is not some crazy region
 
@@ -254,9 +254,11 @@ public class IndelRecordPileCollector implements RecordReceiver {
                 long start = mAllIndels.first().getObject().getStart();
                 long stop = mAllIndels.last().getObject().getStop();
                 System.out.println("Genomic region "+mLastContig+":"+ start + "-"+ stop +
-                                   " was ignored: "+mAllIndels.size() +" unique indels with average distance of "+
+                                   " was ignored: ");
+                System.out.println("   "+mAllIndels.size() +" unique indels with average distance of "+
                                    ((double)(stop - start))/((double)mAllIndels.size()-1) +
                                    " bases between indels");
+                System.out.println("   "+mRecordPile.size() +" reads collected before aborting");
             }
 
             // no indels or avoiding indels in bad region: send all records to defaultReceiver and clear the pile

java/src/org/broadinstitute/sting/playground/utils/TrioConcordanceRecord.java

@@ -19,6 +19,15 @@ public class TrioConcordanceRecord {
 	public int inconsistent_indels_in_parent  = 0 ;
 	public int inconsistent_indels_in_kid  = 0 ;
 	public int non_biallelic = 0; // number of variant calls that are not biallelic
+	public long mom_assessed = 0; // number of assessed loci for mother (i.e. passing confidence threshold filter)
+	public long dad_assessed = 0;
+	public long kid_assessed = 0;
+	public long mom_ref = 0; // number of reference calls (out of total assessed)
+	public long dad_ref = 0;
+	public long kid_ref = 0;
+	public long mom_snp = 0; // number of snp calls (out of total assessed)
+	public long dad_snp = 0;
+	public long kid_snp = 0;
 	
 	public TrioConcordanceRecord add(TrioConcordanceRecord other) {
 		this.assessed_loci += other.assessed_loci;
@@ -32,6 +41,15 @@ public class TrioConcordanceRecord {
 		this.inconsistent_indels_in_parent += other.inconsistent_indels_in_parent;
 		this.inconsistent_indels_in_kid += other.inconsistent_indels_in_kid;
 		this.non_biallelic += other.non_biallelic;
+		this.mom_assessed += other.mom_assessed;
+		this.dad_assessed += other.dad_assessed;
+		this.kid_assessed += other.kid_assessed;
+		this.mom_ref += other.mom_ref;
+		this.dad_ref += other.dad_ref;
+		this.kid_ref += other.kid_ref;
+		this.mom_snp += other.mom_snp;
+		this.dad_snp += other.dad_snp;
+		this.kid_snp += other.kid_snp;
 		
 		return this;
 	}
@@ -39,8 +57,11 @@ public class TrioConcordanceRecord {
 	public int totalSNP() { return consistent_snp + inconsistent_snp + non_biallelic; }
 	
 	public String toString() {
-		return String.format("assessed: %d; reference: %d (%3.2f);  total snp: %d;  consistent snp: %d (%3.2f); multiallelic: %d (%3.2f); " , 
+		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" , 
 				assessed_loci, consistent_ref, ((double)consistent_ref*100.00)/assessed_loci,totalSNP(), consistent_snp, ((double)consistent_snp*100.0)/totalSNP(),
-				non_biallelic, ((double)non_biallelic*100.0)/totalSNP());
+				non_biallelic, ((double)non_biallelic*100.0)/totalSNP(),mom_assessed,dad_assessed,kid_assessed);
+//		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)" , 
+//				assessed_loci, consistent_ref, ((double)consistent_ref*100.00)/assessed_loci,totalSNP(), consistent_snp, ((double)consistent_snp*100.0)/totalSNP(),
+//				non_biallelic, ((double)non_biallelic*100.0)/totalSNP());
 	}
 }