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Uses the new FastaSequenceFile2 for high-performance seeks. 

Added far superior error checking (and reporting!) messages for incorrect usage of the location string.  Prevents users from seeing complex FunctionalJ error message

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@140 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-22 19:56:54 +00:00
parent e77d735e08
commit 611ab0bdb3
1 changed files with 19 additions and 13 deletions
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32
core/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
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@ -59,8 +59,9 @@ public class TraversalEngine {
// The reference data -- filename, refSeqFile, and iterator // The reference data -- filename, refSeqFile, and iterator
private File refFileName = null; // the name of the reference file private File refFileName = null; // the name of the reference file
private ReferenceSequenceFile refFile = null; //private ReferenceSequenceFile refFile = null;
private ReferenceIterator refIter = null; private FastaSequenceFile2 refFile = null; // todo: merge FastaSequenceFile2 into picard!
private ReferenceIterator refIter = null;
// Number of records (loci, reads) we've processed // Number of records (loci, reads) we've processed
private long nRecords = 0; private long nRecords = 0;
@ -199,14 +200,17 @@ public class TraversalEngine {
StdReflect reflect = new JdkStdReflect(); StdReflect reflect = new JdkStdReflect();
FunctionN<GenomeLoc> parseOne = reflect.staticFunction(GenomeLoc.class, "parseGenomeLoc", String.class); FunctionN<GenomeLoc> parseOne = reflect.staticFunction(GenomeLoc.class, "parseGenomeLoc", String.class);
Function1<GenomeLoc, String> f1 = parseOne.f1(); Function1<GenomeLoc, String> f1 = parseOne.f1();
Collection<GenomeLoc> result = Functions.map(f1, Arrays.asList(str.split(";"))); try {
GenomeLoc[] locs = (GenomeLoc[])result.toArray(new GenomeLoc[0]); Collection<GenomeLoc> result = Functions.map(f1, Arrays.asList(str.split(";")));
GenomeLoc[] locs = (GenomeLoc[])result.toArray(new GenomeLoc[0]);
Arrays.sort(locs); Arrays.sort(locs);
System.out.printf(" Locations are: %s%n", Utils.join("\n", Functions.map( Operators.toString, Arrays.asList(locs) ) ) ); System.out.printf(" Locations are: %s%n", Utils.join("\n", Functions.map( Operators.toString, Arrays.asList(locs) ) ) );
return locs;
return locs; } catch ( Exception e ) {
} Utils.scareUser(String.format("Invalid locations string: %s, format is loc1;loc2; where each locN can be 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'", str));
return null;
}
}
/** /**
* A key function that returns true if the proposed GenomeLoc curr is within the list of * A key function that returns true if the proposed GenomeLoc curr is within the list of
@ -337,8 +341,6 @@ public class TraversalEngine {
// Initial the reference ordered data iterators // Initial the reference ordered data iterators
initializeRODs(); initializeRODs();
//testReference();
//loadReference();
return true; return true;
} }
@ -401,7 +403,8 @@ public class TraversalEngine {
*/ */
protected void initializeReference() { protected void initializeReference() {
if ( refFileName != null ) { if ( refFileName != null ) {
this.refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFileName); //this.refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFileName);
this.refFile = new FastaSequenceFile2(refFileName); // todo: replace when FastaSequenceFile2 is in picard
this.refIter = new ReferenceIterator(this.refFile); this.refIter = new ReferenceIterator(this.refFile);
if ( ! Utils.setupRefContigOrdering(this.refFile) ) { if ( ! Utils.setupRefContigOrdering(this.refFile) ) {
// We couldn't process the reference contig ordering, fail since we need it // We couldn't process the reference contig ordering, fail since we need it
@ -424,6 +427,9 @@ public class TraversalEngine {
return rodIters; return rodIters;
} }
/**
* An inappropriately placed testing of reading the reference
*/
protected void testReference() { protected void testReference() {
while (true) { while (true) {
ReferenceSequence ref = refFile.nextSequence(); ReferenceSequence ref = refFile.nextSequence();