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allow contig names to have spaces in the fai. This is not yet supported by samtools fai generator (which truncates at the first space), but we might as well fix it on our side. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1022 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-06-16 22:23:12 +00:00
parent 6ee64c7e43
commit 78b7fb25c7
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
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@ -48,7 +48,7 @@ public class FastaSequenceIndex implements Iterable {
while( scanner.hasNext() ) {
// Tokenize and validate the index line.
String result = scanner.findInLine("([\\w\\.]+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)");
String result = scanner.findInLine("([\\w\\s\\.]+)\\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();