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Merge pull request #1009 from broadinstitute/gg_patch_depthofcoverage_#1002 

User (mnw21cam) patch to fix DoC slowdown in 3.4
This commit is contained in:
Geraldine Van der Auwera 2015-06-10 11:16:08 -04:00
parent aad89cd653 95f2899f05
commit 2a7f95eddb
1 changed files with 16 additions and 3 deletions
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19
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/CoverageUtils.java
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@ -137,6 +137,9 @@ public class CoverageUtils {
public static Map<SAMReadGroupRecord,int[]> getBaseCountsByReadGroup(AlignmentContext context, int minMapQ, int maxMapQ, byte minBaseQ, byte maxBaseQ, CountPileupType countType) { public static Map<SAMReadGroupRecord,int[]> getBaseCountsByReadGroup(AlignmentContext context, int minMapQ, int maxMapQ, byte minBaseQ, byte maxBaseQ, CountPileupType countType) {
Map<SAMReadGroupRecord, int[]> countsByRG = new HashMap<SAMReadGroupRecord,int[]>(); Map<SAMReadGroupRecord, int[]> countsByRG = new HashMap<SAMReadGroupRecord,int[]>();
Map<String, int[]> countsByRGName = new HashMap<String, int[]>();
Map<String, SAMReadGroupRecord> RGByName = new HashMap<String, SAMReadGroupRecord>();
List<PileupElement> countPileup = new LinkedList<PileupElement>(); List<PileupElement> countPileup = new LinkedList<PileupElement>();
FragmentCollection<PileupElement> fpile; FragmentCollection<PileupElement> fpile;
@ -202,10 +205,20 @@ public class CoverageUtils {
for (PileupElement e : countPileup) { for (PileupElement e : countPileup) {
SAMReadGroupRecord readGroup = getReadGroup(e.getRead()); SAMReadGroupRecord readGroup = getReadGroup(e.getRead());
if (!countsByRG.keySet().contains(readGroup))
countsByRG.put(readGroup, new int[6]);
updateCounts(countsByRG.get(readGroup), e); String readGroupId = readGroup.getSample() + "_" + readGroup.getReadGroupId();
int[] counts = countsByRGName.get(readGroupId);
if (counts == null) {
counts = new int[6];
countsByRGName.put(readGroupId, counts);
RGByName.put(readGroupId, readGroup);
}
updateCounts(counts, e);
}
for (String readGroupId : RGByName.keySet()) {
countsByRG.put(RGByName.get(readGroupId), countsByRGName.get(readGroupId));
} }
return countsByRG; return countsByRG;