Searched refs:clipSum (Results 1 – 3 of 3) sorted by relevance
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/transformers/ |
| H A D | BaseQualityClipReadTransformer.java | 42 int clipSum = 0, lastMax = -1, clipPoint = -1; // -1 means no clip in getRightClipPoint() local
45 clipSum += (qTrimmingThreshold - quals[i]); in getRightClipPoint()
46 if (clipSum >= 0 && (clipSum >= lastMax)) { in getRightClipPoint()
47 lastMax = clipSum; in getRightClipPoint()
58 int clipSum = 0, lastMax = -1, clipPoint = -1; // -1 means no clip in getLeftClipPoint() local
61 clipSum += (qTrimmingThreshold - quals[i]); in getLeftClipPoint()
62 if (clipSum >= 0 && (clipSum >= lastMax)) { in getLeftClipPoint()
63 lastMax = clipSum; in getLeftClipPoint()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/ |
| H A D | ClipReads.java | 458 int clipSum = 0, lastMax = -1, clipPoint = -1; // -1 means no clip in clipBadQualityScores() local
462 clipSum += (qTrimmingThreshold - qual); in clipBadQualityScores()
463 if (clipSum >= 0 && (clipSum >= lastMax)) { in clipBadQualityScores()
464 lastMax = clipSum; in clipBadQualityScores()
|
| /dports/biology/bbmap/bbmap/current/shared/ |
| H A D | ReadStats.java | 67 clipSum=new long[2][MAXLEN]; in ReadStats()
75 clipSum=null; in ReadStats()
214 x.clipSum[0][i]+=rs.clipSum[0][i]; in mergeAll()
215 x.clipSum[1][i]+=rs.clipSum[1][i]; in mergeAll()
627 ss=subSum[pairnum], ns=nSum[pairnum], cs=clipSum[pairnum], os=otherSum[pairnum]; in addToMatchHistogram2()
1157 ss1=subSum[0], ns1=nSum[0], cs1=clipSum[0], os1=otherSum[0]; in writeMatchToFile()
1159 ss2=subSum[1], ns2=nSum[1], cs2=clipSum[1], os2=otherSum[1]; in writeMatchToFile()
1189 ss1=subSum[0], ns1=nSum[0], cs1=clipSum[0], os1=otherSum[0]; in writeMatchToFileUnpaired()
1545 public final long[][] clipSum; field in ReadStats
|