Merge branch 'master' into phasing

compgen-io · Nov 2, 2021 · 3407743 · 3407743
2 parents c607f9d + 596f53c
commit 3407743
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Showing 4 changed files with 29 additions and 3 deletions.
diff --git a/src/java/io/compgen/ngsutils/NGSUtils.java b/src/java/io/compgen/ngsutils/NGSUtils.java
@@ -216,7 +216,7 @@ public static void main(String[] args) {
 			.addCommand(VCFPeptide.class)
 			.addCommand(FastaGrep.class)
 			.addCommand(BamToFasta.class)
-			.addCommand(BamPhase.class);
+			.addCommand(BamPhase.class)
 
         try {
             if (args.length == 0) {

diff --git a/src/java/io/compgen/ngsutils/bam/support/ReadUtils.java b/src/java/io/compgen/ngsutils/bam/support/ReadUtils.java
@@ -529,6 +529,7 @@ public static SAMRecord removeClipping(SAMRecord read, boolean writeFlags) throw
 	public static SAMRecord findMate(SamReader reader, SAMRecord read) {
 		return findMate(reader, read, 0, 0);
 	}
+
 	public static SAMRecord findMate(SamReader reader, SAMRecord read, int filterFlags, int requiredFlags) {
         if (!read.getReadPairedFlag()) {
             throw new IllegalArgumentException("findMate requires paired end reads!");
@@ -543,7 +544,6 @@ public static SAMRecord findMate(SamReader reader, SAMRecord read, int filterFla
         }
 
         while (it.hasNext() && mate == null) {
-
             SAMRecord q = it.next();
             if (filterFlags > 0) {
             	if ((q.getFlags() & filterFlags) != 0) {
@@ -589,6 +589,7 @@ public static SAMRecord findMate(SamReader reader, SAMRecord read, int filterFla
             		}
             	}
             	if (found) {
+                // this won't happen because we break out of the while loop first
 //            		if (mate != null) {
 //                        throw new IllegalArgumentException("findMate found multiple records for read: "+read.getReadName());
 //            		}
@@ -599,7 +600,8 @@ public static SAMRecord findMate(SamReader reader, SAMRecord read, int filterFla
         it.close();
 		return mate;
 	}
-
+
+  // Does a read contain a particular variant?
 	public static boolean containsVariant(SAMRecord read, VCFRecord rec, String allele, IndexedFastaFile fasta) throws IOException {
 		if (!read.getReferenceName().equals(rec.getChrom())) {
 			return false;

diff --git a/src/java/io/compgen/ngsutils/cli/bam/BamExtract.java b/src/java/io/compgen/ngsutils/cli/bam/BamExtract.java
@@ -341,10 +341,24 @@ public void exec() throws IOException, VCFParseException, CommandArgumentExcepti
         	extractReads(region.ref, region.start, region.end);
         } else if (bedFile != null) {
         	Iterator<BedRecord> it = BedReader.readFile(bedFile);
+//        	int lastRecLen = 0;
+
         	while (it.hasNext()) {
         		BedRecord rec = it.next();
+//        		for (int i=0; i<lastRecLen;i++) {
+//        			System.err.write('\b');
+//        		}
+//        		for (int i=0; i<lastRecLen;i++) {
+//        			System.err.write(' ');
+//        		}
+//        		for (int i=0; i<lastRecLen;i++) {
+//        			System.err.write('\b');
+//        		}
+//        		System.err.print(rec);
+//        		lastRecLen = rec.toString().length();
             	extractReads(rec.getCoord().ref, rec.getCoord().start, rec.getCoord().end, rec.getCoord().strand);
         	}
+        	System.err.println("Done");
         } else if (vcfFile != null) {
         	VCFReader vcfReader = new VCFReader(vcfFile);
         	Iterator<VCFRecord> it = vcfReader.iterator();

diff --git a/src/java/io/compgen/ngsutils/cli/vcf/VCFAnnotateCmd.java b/src/java/io/compgen/ngsutils/cli/vcf/VCFAnnotateCmd.java
@@ -273,6 +273,16 @@ public void setInfoInFile(String val) throws CommandArgumentException {
     }
 
 
+//    @Option(desc="Add peptide annotation for SNVs", name="gtf", helpValue="filename.gtf")
+//    public void setGTFPeptide(String filename) throws CommandArgumentException {
+//		try {
+//			chain.add(new GTFGene(filename));
+//		} catch (IOException e) {
+//			throw new CommandArgumentException(e);
+//		}    	
+//    }
+
+
     @Option(desc="Add gene annotations (INFO: CG_GENE, CG_GENE_STRAND, CG_GENE_REGION)", name="gtf", helpValue="filename.gtf")
     public void setGTF(String filename) throws CommandArgumentException {
 		try {