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seekForwardOffset changed (improved?): first, compareContigs does *not*, in general, return -1,0 or 1 if no dictionary is available; second, be more flexible in trying to jump to the right contig (current implementation of FastaFile2 will still through an exception if there's no dictionary, but iterator itself behaves transparently) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@317 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-07 21:42:33 +00:00
parent 2663ac3e4a
commit b64e4d1a04
1 changed files with 11 additions and 9 deletions
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20
java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
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@ -134,10 +134,10 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
assert seekContigName.equals(currentContig.getName()) : String.format("only works on this contig, but the current %s and sought %s contigs are different!", currentContig.getName(), seekContigName); assert seekContigName.equals(currentContig.getName()) : String.format("only works on this contig, but the current %s and sought %s contigs are different!", currentContig.getName(), seekContigName);
// we're somewhere on this contig // we're somewhere on this contig
if (seekOffset < offset) { if (seekOffset < offset ) {
// bad boy -- can't go backward safely // bad boy -- can't go backward safely
throw new IllegalArgumentException(String.format("Invalid seek %s => %s, which is usually due to out of order reads%n", throw new IllegalArgumentException(String.format("Invalid seek %s => %s, which is usually due to out of order reads%n",
new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(currentContig.getName(), seekOffset))); new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(seekContigName, seekOffset)));
} else if (seekOffset >= currentContig.length()) { } else if (seekOffset >= currentContig.length()) {
// bad boy -- can't go beyond the contig length // bad boy -- can't go beyond the contig length
throw new IllegalArgumentException(String.format("Invalid seek to %s, which is beyond the end of the contig%n", throw new IllegalArgumentException(String.format("Invalid seek to %s, which is beyond the end of the contig%n",
@ -161,20 +161,22 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
logger.debug(String.format(" -> Seeking to %s %d from %s %d%n", seekContigName, seekOffset, currentContig.getName(), offset)); logger.debug(String.format(" -> Seeking to %s %d from %s %d%n", seekContigName, seekOffset, currentContig.getName(), offset));
int cmpContigs = GenomeLoc.compareContigs(seekContigName, currentContig.getName()); int cmpContigs = GenomeLoc.compareContigs(seekContigName, currentContig.getName());
if (cmpContigs == -1 && false) { // todo: fixed if ( cmpContigs < 0 && GenomeLoc.hasKnownContigOrdering() ) { // if we know the order of contigs and we are already past the contig we seek, it's too late!
// The contig we are looking for is before the currentContig -- it's an error // The contig we are looking for is before the currentContig -- it's an error
throw new IllegalArgumentException(String.format("Invalid seek %s => %s, which is usually due to out of order reads%n", throw new IllegalArgumentException(String.format("Invalid seek %s => %s, contigs/sequences are out of order%n",
new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(currentContig.getName(), seekOffset))); new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(seekContigName, seekOffset)));
} else if (cmpContigs == 1) { }
// we need to jump forward
if ( cmpContigs > 0 || (! GenomeLoc.hasKnownContigOrdering() ) && cmpContigs != 0 ) { // if contig we seek is still ahead, or if we have no idea what the order is and current contig is not what we seek
// then try to seek forward in the reference file until we get the contig we need
if (DEBUG) if (DEBUG)
logger.debug(String.format(" -> Seeking in the fasta file to %s from %s%n", seekContigName, currentContig.getName())); logger.debug(String.format(" -> Seeking in the fasta file to %s from %s%n", seekContigName, currentContig.getName()));
if (!refFile.seekToContig(seekContigName)) { // ok, do the seek if (!refFile.seekToContig(seekContigName)) { // ok, do the seek
// a false result indicates a failure, throw a somewhat cryptic call // a false result indicates a failure, throw a somewhat cryptic call
throw new RuntimeIOException(String.format("Unexpected seek failure from %s to %s%n", throw new RuntimeIOException(String.format("Unexpected seek failure from %s to %s%n",
new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(currentContig.getName(), seekOffset))); new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(seekContigName, seekOffset)));
} }
readNextContig(); // since we haven't failed, we just read in the next contig (which is seekContigName) readNextContig(); // since we haven't failed, we just read in the next contig (which is seekContigName)