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()
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/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()
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/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
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