zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Processing intervals as they stream in means much lower memory usage and 

quicker runtime.  Making change as minimal as possible to avoid conflicts
with BT's incoming patch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3061 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-22 22:04:45 +00:00
parent 0097106938
commit 3767adb0bb
1 changed files with 10 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
View File

@ -252,7 +252,6 @@ public class GenomeLocParser {
* @return the list of merged locations
*/
public static List<GenomeLoc> mergeIntervalLocations(final List<GenomeLoc> raw, IntervalMergingRule rule) {
logger.debug(" Raw locations are: " + Utils.join(", ", raw));
if (raw.size() <= 1 || rule == IntervalMergingRule.NONE)
return raw;
else {
@ -355,11 +354,18 @@ public class GenomeLocParser {
} catch (Exception e) {
try {
ret = new ArrayList<GenomeLoc>();
xReadLines reader = new xReadLines(new File(file_name));
List<String> lines = reader.readLines();
for(String line: reader) {
List<GenomeLoc> loci = parseGenomeLocs(line, rule);
if(loci != null)
ret.addAll(loci);
}
reader.close();
String locStr = Utils.join(";", lines);
ret = parseGenomeLocs(locStr, rule);
if(ret.isEmpty())
return null;
for(GenomeLoc locus: ret)
exceptionOnInvalidGenomeLocBounds(locus);
return ret;