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

Fixed bug in retaining proper RefSeq records 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4768 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2010-12-01 18:39:02 +00:00
parent 7caf666f48
commit 9ac0f98d0d
2 changed files with 24 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
View File

@ -150,6 +150,7 @@ public class MergeSegregatingAlternateAllelesVCFWriter implements VCFWriter {
else { // waiting to merge vcfrWaitingToMerge, and curVcIsNotFiltered. So, attempt to merge them: else { // waiting to merge vcfrWaitingToMerge, and curVcIsNotFiltered. So, attempt to merge them:
numRecordsAttemptToMerge++; numRecordsAttemptToMerge++;
boolean shouldAttemptToMerge = vcMergeRule.shouldAttemptToMerge(vcfrWaitingToMerge.vc, vc); boolean shouldAttemptToMerge = vcMergeRule.shouldAttemptToMerge(vcfrWaitingToMerge.vc, vc);
logger.debug("shouldAttemptToMerge? = " + shouldAttemptToMerge);
/* /*
TODO: -- CONSIDER THE FOLLOWING EXAMPLE: WHAT DO WE WANT HERE??? -- TODO: -- CONSIDER THE FOLLOWING EXAMPLE: WHAT DO WE WANT HERE??? --

33
java/src/org/broadinstitute/sting/gatk/walkers/phasing/RefSeqDataParser.java
View File

@ -46,11 +46,23 @@ public class RefSeqDataParser {
Map<String, String> entriesToNames = new HashMap<String, String>(); Map<String, String> entriesToNames = new HashMap<String, String>();
Integer numRecords = vc.getAttributeAsIntegerNoException(NUM_RECORDS_KEY); Integer numRecords = vc.getAttributeAsIntegerNoException(NUM_RECORDS_KEY);
if (numRecords != null) { if (numRecords != null) {
for (int i = 1; i <= numRecords; i++) { boolean done = false;
String key = nameKeyToUseMultiplePrefix + i;
String name = vc.getAttributeAsStringNoException(key); if (numRecords == 1) { // Check if perhaps the single record doesn't end with "_1":
if (name != null) String name = vc.getAttributeAsStringNoException(nameKeyToUse);
entriesToNames.put(key, name); if (name != null) {
entriesToNames.put(nameKeyToUse, name);
done = true;
}
}
if (!done) {
for (int i = 1; i <= numRecords; i++) {
String key = nameKeyToUseMultiplePrefix + i;
String name = vc.getAttributeAsStringNoException(key);
if (name != null)
entriesToNames.put(key, name);
}
} }
} }
else { // no entry with the # of records: else { // no entry with the # of records:
@ -90,7 +102,7 @@ public class RefSeqDataParser {
Set<String> commonNames = entriesMap1.keySet(); Set<String> commonNames = entriesMap1.keySet();
commonNames.retainAll(entriesMap2.keySet()); commonNames.retainAll(entriesMap2.keySet());
boolean addSuffix = commonNames.size() > 1; boolean addSuffix = commonNames.size() > 1;
int count = 1; int nextCount = 1;
for (String name : commonNames) { for (String name : commonNames) {
RefSeqEntry refseq1 = entriesMap1.get(name); RefSeqEntry refseq1 = entriesMap1.get(name);
@ -98,7 +110,7 @@ public class RefSeqDataParser {
String keySuffix = ""; String keySuffix = "";
if (addSuffix) if (addSuffix)
keySuffix = "_" + count; keySuffix = "_" + nextCount;
boolean added = false; boolean added = false;
for (String key : NAME_KEYS) { for (String key : NAME_KEYS) {
@ -111,10 +123,11 @@ public class RefSeqDataParser {
} }
} }
if (added) if (added)
count++; nextCount++;
} }
if (count > 1) int totalCount = nextCount - 1; // since incremented count one extra time
refSeqNameAttribs.put(NUM_RECORDS_KEY, count - 1); // since incremented count one extra time if (totalCount > 1)
refSeqNameAttribs.put(NUM_RECORDS_KEY, totalCount);
return refSeqNameAttribs; return refSeqNameAttribs;
} }