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Changed the assert code in the genome loc to throw exceptions, and deleted a function no one seems to be using. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@569 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-04-30 13:54:51 +00:00
parent b630f2f2f1
commit 3bf3c21ddd
2 changed files with 33 additions and 60 deletions
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90
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
View File

@ -48,60 +48,23 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
return contigInfo != null;
}
public static GenomeLoc getFirstLocation()
{
assert contigInfo != null && contigInfo.size() != 0;
return new GenomeLoc(contigInfo.getSequence(0).getSequenceName(), 0, 0);
}
public static SAMSequenceRecord getContigInfo( final String contig ) {
return contigInfo.getSequence(contig);
}
public static int getContigIndex( final String contig ) {
assert contigInfo.getSequenceIndex(contig) != -1 : "Unknown contig " + contig;
/**
* Returns the contig index of a specified string version of the contig
* @param contig the contig string
* @return the contig index, -1 if not found
*/
public static int getContigIndex( final String contig ) {
if (contigInfo.getSequenceIndex(contig) == -1)
Utils.scareUser(String.format("Contig %s given as location, but this contig isn't present in the Fasta sequence dictionary", contig));
return contigInfo.getSequenceIndex(contig);
}
/*
public static void setContigOrdering(Map<String, Integer> rco) {
refContigOrdering = rco;
interns = new HashMap<String, String>();
for ( String contig : rco.keySet() )
interns.put( contig, contig );
}
*/
/*
public static boolean setupRefContigOrdering(final ReferenceSequenceFile refFile) {
final SAMSequenceDictionary seqDict = refFile.getSequenceDictionary();
if (seqDict == null) // we couldn't load the reference dictionary
return false;
List<SAMSequenceRecord> refContigs = seqDict.getSequences();
HashMap<String, Integer> refContigOrdering = new HashMap<String, Integer>();
if (refContigs != null) {
int i = 0;
logger.info(String.format("Prepared reference sequence contig dictionary%n order ->"));
for (SAMSequenceRecord contig : refContigs) {
logger.info(String.format(" %s (%d bp)", contig.getSequenceName(), contig.getSequenceLength()));
refContigOrdering.put(contig.getSequenceName(), i);
i++;
}
}
setContigOrdering(refContigOrdering);
return refContigs != null;
}
*/
public static boolean setupRefContigOrdering(final ReferenceSequenceFile refFile) {
return setupRefContigOrdering(refFile.getSequenceDictionary());
}
@ -128,10 +91,13 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
//
// --------------------------------------------------------------------------------------------------------------
public GenomeLoc( int contigIndex, final long start, final long stop ) {
assert contigInfo != null : "No sequence dictionary defined but index was given";
assert contigIndex >= 0 && contigIndex < contigInfo.size() : "ContigIndex " + contigIndex + " is bad " + contigInfo.size();
assert start >= 0 : "Bad start position " + start;
assert stop >= -1 : "Bad stop position " + stop; // a negative -1 indicates it's not a meaningful end position
if(contigInfo == null) { throw new StingException("Contig info has not been setup in the GenomeLoc context yet."); }
if (contigIndex < 0 || contigIndex >= contigInfo.size()) {
throw new StingException("Contig info has not been setup in the GenomeLoc context yet.");
}
if (start < 0) { throw new StingException("Bad start position " + start);}
if (stop < -1) { throw new StingException("Bad stop position " + stop); } // a negative -1 indicates it's not a meaningful end position
this.contigIndex = contigIndex;
this.start = start;
@ -216,7 +182,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
}
if ( bad ) {
throw new RuntimeException("Invalid Genome Location string: " + str);
throw new StingException("Invalid Genome Location string: " + str);
}
if ( stop == Integer.MAX_VALUE && hasKnownContigOrdering() ) {
@ -362,10 +328,17 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
// Accessors and setters
//
public final String getContig() {
assert this.contigIndex != -1;
assert contigInfo.getSequence(this.contigIndex) != null;
assert contigInfo.getSequence(this.contigIndex).getSequenceName() != null;
//this.contigIndex != -1;
if (!(contigInfo != null && contigInfo.getSequences() != null)) {
throw new StingException("The contig information or it's sequences are null");
}
if ((this.contigIndex < 0) || (this.contigIndex >= contigInfo.getSequences().size())) {
throw new StingException("The contig index is not bounded by the zero and seqeunce count, contig index: " + contigIndex);
}
if (contigInfo.getSequence(this.contigIndex) == null ||
contigInfo.getSequence(this.contigIndex).getSequenceName() == null) {
throw new StingException("The associated sequence index for contig " + contigIndex + " is null");
}
return contigInfo.getSequence(this.contigIndex).getSequenceName();
//if (contigInfo != null && contigInfo.getSequence(this.contigIndex) != null) {
// return contigInfo.getSequence(this.contigIndex).getSequenceName();
@ -425,8 +398,10 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
return ! discontinuousP( that );
}
public GenomeLoc merge( GenomeLoc that ) {
assert this.contiguousP(that);
public GenomeLoc merge( GenomeLoc that ) throws StingException {
if (!(this.contiguousP(that))) {
throw new StingException("The two genome loc's need to be contigous");
}
return new GenomeLoc(getContig(),
Math.min(getStart(), that.getStart()),
@ -488,9 +463,6 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
return 0;
}
//assert getContigIndex(thisContig) != -1;// : this;
//assert getContigIndex(thatContig) != -1;// : that;
if ( hasKnownContigOrdering() )
{
int thisIndex = getContigIndex(thisContig);
@ -582,7 +554,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
return ret;
} catch (Exception e2) {
e2.printStackTrace();
throw new IllegalArgumentException(e);
throw new StingException("Unable to parse out interval file in either format", e);
}
}
}

3
java/test/org/broadinstitute/sting/utils/GenomeLocTest.java
View File

@ -22,6 +22,7 @@ public class GenomeLocTest extends BaseTest {
public static void init() {
// sequence
seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
GenomeLoc.setupRefContigOrdering(seq);
}
/**
@ -30,7 +31,7 @@ public class GenomeLocTest extends BaseTest {
@Test
public void testIsBetween() {
logger.warn("Executing testIsBetween");
GenomeLoc.setupRefContigOrdering(seq);
GenomeLoc locMiddle = new GenomeLoc("chr1", 3, 3);
GenomeLoc locLeft = new GenomeLoc("chr1", 1, 1);