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Safer interface for ReorderSam. Better error checking. Documentation. Moving into Picard now 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5283 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-02-20 14:35:44 +00:00
parent 463bb737c3
commit aa4a4e515d
1 changed files with 69 additions and 14 deletions
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83
java/src/org/broadinstitute/sting/playground/tools/ReorderSam.java
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@ -25,8 +25,10 @@ public class ReorderSam extends CommandLineProgram {
public File OUT = null;
@Option(shortName="R", doc="Reference sequence to reorder reads to match", optional=false)
public File REFERENCE = null;
@Option(shortName="S", doc="If true, then every contig in the reads must be present in the new reference sequence. By default, reads without a corresponding contig in the new reference are made unmapped", optional=true)
public Boolean REQUIRE_COMPLETE_DICT_CONCORDANCE = false;
@Option(shortName="S", doc="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs. By default, this tool requires a corresponding contig in the new reference for each read contig", optional=true)
public Boolean ALLOW_INCOMPLETE_DICT_CONCORDANCE = false;
@Option(shortName="U", doc="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length. Highly dangerous, only use if you know what you are doing.", optional=true)
public Boolean ALLOW_CONTIG_LENGTH_DISCORDANCE = false;
/** Required main method implementation. */
public static void main(final String[] argv) {
@ -45,7 +47,6 @@ public class ReorderSam extends CommandLineProgram {
System.exit(1);
}
printDictionary("SAM/BAM file", inReader.getFileHeader().getSequenceDictionary());
printDictionary("Reference", refDict);
Map<Integer, Integer> newOrder = buildSequenceDictionaryMap(refDict, inReader.getFileHeader().getSequenceDictionary());
@ -55,19 +56,33 @@ public class ReorderSam extends CommandLineProgram {
outHeader.setSequenceDictionary(refDict);
SAMFileWriter outWriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, true, OUT) ;
//
// write the reads in contig order
//
System.out.println("Writing reads...");
for ( SAMSequenceRecord contig : refDict.getSequences() ) {
System.out.println("Writing reads on contig " + contig.getSequenceName());
writeReads(outWriter, inReader.query(contig.getSequenceName(), 0, 0, false), newOrder);
SAMRecordIterator it = inReader.query(contig.getSequenceName(), 0, 0, false);
writeReads(outWriter, it, newOrder, contig.getSequenceName());
}
// write the unmapped reads
writeReads( outWriter, inReader.queryUnmapped(), newOrder);
// don't forget the unmapped reads
writeReads( outWriter, inReader.queryUnmapped(), newOrder, "unmapped" );
// cleanup
inReader.close();
outWriter.close();
return 0;
}
/**
* Low-level helper function that returns the new reference index for oldIndex according to the
* ordering map newOrder. Read is provided in case an error occurs, so that an informative message
* can be made.
*
* @param read
* @param oldIndex
* @param newOrder
* @return
*/
private static int newOrderIndex(SAMRecord read, int oldIndex, Map<Integer, Integer> newOrder) {
if ( oldIndex == -1 )
return -1; // unmapped read
@ -77,9 +92,24 @@ public class ReorderSam extends CommandLineProgram {
return newOrder.get(oldIndex);
}
private static void writeReads(SAMFileWriter out, SAMRecordIterator it, Map<Integer, Integer> newOrder) {
/**
* Helper function that writes reads from iterator it into writer out, updating each SAMRecord along the way
* according to the newOrder mapping from dictionary index -> index. Name is used for printing only.
*
* @param out
* @param it
* @param newOrder
* @param name
*/
private static void writeReads(SAMFileWriter out, SAMRecordIterator it, Map<Integer, Integer> newOrder, String name) {
long counter = 0;
System.out.print(" Processing " + name);
System.out.flush();
while ( it.hasNext() ) {
counter++;
SAMRecord read = it.next();
read.setHeader(out.getFileHeader());
//System.out.println("Writing read " + read.format());
int oldRefIndex = read.getReferenceIndex();
@ -96,16 +126,37 @@ public class ReorderSam extends CommandLineProgram {
out.addAlignment(read);
}
it.close();
System.out.println(" => Wrote " + counter + " reads");
}
/**
* Constructs a mapping from read sequence records index -> new sequence dictionary index for use in
* reordering the reference index and mate reference index in each read. -1 means unmapped.
* @param refDict
* @param readsDict
* @return
*/
private Map<Integer, Integer> buildSequenceDictionaryMap(SAMSequenceDictionary refDict, SAMSequenceDictionary readsDict) {
Map<Integer, Integer> newOrder = new HashMap<Integer, Integer>();
System.out.println("Reordering SAM/BAM file:");
for ( SAMSequenceRecord refRec : refDict.getSequences() ) {
SAMSequenceRecord readsRec = readsDict.getSequence(refRec.getSequenceName());
if ( readsRec != null ) {
System.out.printf("Mapping %s [%d] => %s [%d]%n",
if ( refRec.getSequenceLength() != readsRec.getSequenceLength() ) {
String msg = String.format("Discordant contig lengths: read %s LN=%d, ref %s LN=%d",
readsRec.getSequenceName(), readsRec.getSequenceLength(),
refRec.getSequenceName(), refRec.getSequenceLength());
if ( ALLOW_CONTIG_LENGTH_DISCORDANCE ) {
System.err.println("WARN: " + msg);
} else {
throw new PicardException(msg);
}
}
System.out.printf(" Reordering read contig %s [index=%d] to => ref contig %s [index=%d]%n",
readsRec.getSequenceName(), readsRec.getSequenceIndex(),
refRec.getSequenceName(), refRec.getSequenceIndex());
newOrder.put(readsRec.getSequenceIndex(), refRec.getSequenceIndex());
@ -114,21 +165,25 @@ public class ReorderSam extends CommandLineProgram {
for ( SAMSequenceRecord readsRec : readsDict.getSequences() ) {
if ( ! newOrder.containsKey(readsRec.getSequenceIndex()) ) {
if ( REQUIRE_COMPLETE_DICT_CONCORDANCE )
throw new PicardException("No matching contig in new reference found for " + readsRec.getSequenceName());
else
if ( ALLOW_INCOMPLETE_DICT_CONCORDANCE )
newOrder.put(readsRec.getSequenceIndex(), -1);
else
throw new PicardException("New reference sequence does not contain a matching contig for " + readsRec.getSequenceName());
}
}
return newOrder;
}
/**
* Helper function to print out a sequence dictionary
* @param name
* @param dict
*/
private static void printDictionary(String name, SAMSequenceDictionary dict) {
System.out.println(name);
for ( SAMSequenceRecord contig : dict.getSequences() ) {
System.out.println(contig.getSequenceName());
System.out.printf( " SN=%s LN=%d%n", contig.getSequenceName(), contig.getSequenceLength());
}
}
}