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fix for bug GSA-234: fasta index files couldn't handle anything but letters, numbers, or spaces in the contig name 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2147 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-11-24 19:19:47 +00:00
parent 3fca23cd16
commit 8fbc0c8473
2 changed files with 64 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
View File

@ -47,8 +47,8 @@ public class FastaSequenceIndex implements Iterable {
Scanner scanner = new Scanner(indexFile);
while( scanner.hasNext() ) {
// Tokenize and validate the index line.
String result = scanner.findInLine("([\\w\\s\\.]+)\\t+(\\d+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)");
// Tokenize and validate the index line.
String result = scanner.findInLine("(.+)\\t+(\\d+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)");
if( result == null )
throw new PicardException("Found invalid line in index file:" + scanner.nextLine());
MatchResult tokens = scanner.match();

62
java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java
View File

@ -19,17 +19,25 @@ import java.util.Iterator;
* To change this template use File | Settings | File Templates.
*/
public class FastaSequenceIndexTest extends BaseTest {
// our basic human 18 fai
private static String sequenceIndexName = null;
private FastaSequenceIndex sequenceIndex = null;
// a custom index that tests the colon, and semi-colon, and other random characters
private static String sequenceIndexColonSemiColonTestName = null;
private FastaSequenceIndex sequenceIndexColonSemiColonTest = null;
@BeforeClass
public static void initialize() {
sequenceIndexName = seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta.fai";
sequenceIndexColonSemiColonTestName = "/humgen/gsa-scr1/GATK_Data/Validation_Data/testing.fai";
}
@Before
public void doForEachTest() throws FileNotFoundException {
sequenceIndex = new FastaSequenceIndex( new File(sequenceIndexName) );
sequenceIndexColonSemiColonTest = new FastaSequenceIndex( new File(sequenceIndexColonSemiColonTestName) );
}
@Test
@ -189,4 +197,58 @@ public class FastaSequenceIndexTest extends BaseTest {
Assert.assertEquals("Contig chrX_random is not present", "chrX_random", sequenceIndexEntries.next().getContig());
Assert.assertFalse("Iterator still has more entries", sequenceIndexEntries.hasNext());
}
@Test
public void testSpecialCharacters() {
/* file contents:
chrM 16571 6 50 51
chr1;boat 247249719 16915 50 51
chr2:money 242951149 252211635 50 51
chr3::; 199501827 500021813 50 51
;;;;;; 1234 1234 1234 1234
file:gi|17981852|ref|NC_001807.4| 16571 2911876801 70 71
*/
Iterator<FastaSequenceIndexEntry> sequenceIndexEntries = sequenceIndexColonSemiColonTest.iterator();
FastaSequenceIndexEntry ent = sequenceIndexEntries.next();
Assert.assertEquals("Contig chrM is not present","chrM",ent.getContig());
Assert.assertEquals("Contig chrM size is not correct",16571,ent.getSize());
Assert.assertEquals("Contig chrM location is not correct",6,ent.getLocation());
Assert.assertEquals("Contig chrM bases per line is not correct",50,ent.getBasesPerLine());
Assert.assertEquals("Contig chrM bytes per line is not correct",51,ent.getBytesPerLine());
ent = sequenceIndexEntries.next();
Assert.assertEquals("Contig chr1;boat is not present","chr1;boat",ent.getContig());
Assert.assertEquals("Contig chr1;boat size is not correct",247249719,ent.getSize());
Assert.assertEquals("Contig chr1;boat location is not correct",16915,ent.getLocation());
Assert.assertEquals("Contig chr1;boat bases per line is not correct",50,ent.getBasesPerLine());
Assert.assertEquals("Contig chr1;boat bytes per line is not correct",51,ent.getBytesPerLine());
ent = sequenceIndexEntries.next();
Assert.assertEquals("Contig chr2:money is not present","chr2:money",ent.getContig());
Assert.assertEquals("Contig chr2:money size is not correct",242951149,ent.getSize());
Assert.assertEquals("Contig chr2:money location is not correct",252211635,ent.getLocation());
Assert.assertEquals("Contig chr2:money bases per line is not correct",50,ent.getBasesPerLine());
Assert.assertEquals("Contig chr2:money bytes per line is not correct",51,ent.getBytesPerLine());
ent = sequenceIndexEntries.next();
Assert.assertEquals("Contig chr3::; is not present","chr3::;",ent.getContig());
Assert.assertEquals("Contig chr3::; size is not correct",199501827,ent.getSize());
Assert.assertEquals("Contig chrM location is not correct",500021813,ent.getLocation());
Assert.assertEquals("Contig chr3::; bases per line is not correct",50,ent.getBasesPerLine());
Assert.assertEquals("Contig chr3::; bytes per line is not correct",51,ent.getBytesPerLine());
ent = sequenceIndexEntries.next();
Assert.assertEquals("Contig ;;;;;;;; is not present",";;;;;;;;",ent.getContig());
Assert.assertEquals("Contig ;;;;;;;; size is not correct",123,ent.getSize());
Assert.assertEquals("Contig ;;;;;;;; location is not correct",234,ent.getLocation());
Assert.assertEquals("Contig ;;;;;;;; bases per line is not correct",456,ent.getBasesPerLine());
Assert.assertEquals("Contig ;;;;;;;; bytes per line is not correct",789,ent.getBytesPerLine());
ent = sequenceIndexEntries.next();
Assert.assertEquals("Contig file:gi|17981852|ref|NC_001807.4| is not present","file:gi|17981852|ref|NC_001807.4|",ent.getContig());
Assert.assertEquals("Contig file:gi|17981852|ref|NC_001807.4| size is not correct",16571,ent.getSize());
Assert.assertEquals("Contig file:gi|17981852|ref|NC_001807.4| location is not correct",2911876801L,ent.getLocation());
Assert.assertEquals("Contig file:gi|17981852|ref|NC_001807.4| bases per line is not correct",70,ent.getBasesPerLine());
Assert.assertEquals("Contig file:gi|17981852|ref|NC_001807.4| bytes per line is not correct",71,ent.getBytesPerLine());
}
}