From eca0833ebb851d93c7f3020b97113b0d9a566ddb Mon Sep 17 00:00:00 2001 From: Charles Shale Date: Mon, 9 Sep 2024 11:50:52 +1000 Subject: [PATCH] Redux: rename only --- .../hmftools/redux/common/DuplicateGroup.java | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/redux/src/main/java/com/hartwig/hmftools/redux/common/DuplicateGroup.java b/redux/src/main/java/com/hartwig/hmftools/redux/common/DuplicateGroup.java index aada25d28e..820ea941f7 100644 --- a/redux/src/main/java/com/hartwig/hmftools/redux/common/DuplicateGroup.java +++ b/redux/src/main/java/com/hartwig/hmftools/redux/common/DuplicateGroup.java @@ -1,17 +1,12 @@ package com.hartwig.hmftools.redux.common; -import static java.lang.Math.max; -import static java.lang.Math.min; import static java.lang.String.format; -import static com.hartwig.hmftools.common.region.BaseRegion.positionWithin; import static com.hartwig.hmftools.common.bam.SamRecordUtils.addConsensusReadAttribute; import static com.hartwig.hmftools.common.bam.SamRecordUtils.getFivePrimeUnclippedPosition; import static com.hartwig.hmftools.common.bam.SamRecordUtils.orientation; import static com.hartwig.hmftools.common.bam.UmiReadType.DUAL; import static com.hartwig.hmftools.common.bam.UmiReadType.SINGLE; -import static com.hartwig.hmftools.common.utils.sv.StartEndIterator.SE_END; -import static com.hartwig.hmftools.common.utils.sv.StartEndIterator.SE_START; import static com.hartwig.hmftools.common.utils.sv.SvCommonUtils.POS_ORIENT; import static com.hartwig.hmftools.redux.ReduxConfig.RD_LOGGER; import static com.hartwig.hmftools.redux.common.FragmentStatus.DUPLICATE; @@ -149,7 +144,8 @@ else if(!read.getSupplementaryAlignmentFlag() && hasValidSupp) public void addRead(final SAMRecord read) { - int readTypeIndex = getReadTypeIndex(read); + ReadType readType = getReadTypeIndex(read); + int readTypeIndex = readType.ordinal(); if(mReadGroups[readTypeIndex] == null) mReadGroups[readTypeIndex] = Lists.newArrayListWithExpectedSize(mFragmentCount); @@ -227,22 +223,22 @@ public String toString() } } - private int getReadTypeIndex(final SAMRecord read) + private ReadType getReadTypeIndex(final SAMRecord read) { if(!read.getSupplementaryAlignmentFlag()) { // determine if matches the designed initial read or its mate boolean matchesInitial = matchesInitialPrimaryRead(read); - return matchesInitial ? ReadType.INITIAL_PRIMARY.ordinal() : ReadType.MATE.ordinal(); + return matchesInitial ? ReadType.INITIAL_PRIMARY : ReadType.MATE; } else { Boolean isInitialRead = mReadIdInitialIsFirst.get(read.getReadName()); if(isInitialRead == null) - return ReadType.INITIAL_SUPPLEMENTARY.ordinal(); // should not happen since primaries are processed first + return ReadType.INITIAL_SUPPLEMENTARY; // should not happen since primaries are processed first - return isInitialRead == read.getFirstOfPairFlag() ? ReadType.INITIAL_SUPPLEMENTARY.ordinal() : ReadType.MATE_SUPPLEMENTARY.ordinal(); + return isInitialRead == read.getFirstOfPairFlag() ? ReadType.INITIAL_SUPPLEMENTARY : ReadType.MATE_SUPPLEMENTARY; } }