From b12080fb33e96705c92f45dc80e19cdd63844347 Mon Sep 17 00:00:00 2001 From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04> Date: Tue, 15 Mar 2011 14:37:39 +0000 Subject: [PATCH] fix for reverse strand git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15722 ee4ac58c-ac51-4696-9907-e4b3aa274f04 --- uk/ac/sanger/artemis/components/variant/IOUtils.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/uk/ac/sanger/artemis/components/variant/IOUtils.java b/uk/ac/sanger/artemis/components/variant/IOUtils.java index 601d55471..fa4010344 100644 --- a/uk/ac/sanger/artemis/components/variant/IOUtils.java +++ b/uk/ac/sanger/artemis/components/variant/IOUtils.java @@ -405,11 +405,12 @@ class IOUtils if(i+MAX_BASE_CHUNK-1 > length) sendc = send; + int sbegc_raw = sbegc; + int sendc_raw = sendc; if(direction == Bases.REVERSE) { - int tmp = sendc; - sendc = bases.getLength () - sbegc + 1; - sbegc = bases.getLength () - tmp + 1; + sendc = bases.getLength () - sbegc_raw + 1; + sbegc = bases.getLength () - sendc_raw + 1; } MarkerRange m = new MarkerRange(marker.getStrand(), sbegc, sendc); @@ -417,7 +418,7 @@ class IOUtils FeatureVector features = entryGroup.getFeaturesInRange(m.getRange()); //System.out.println((reader == null ? "" : reader.getName())+" "+sbegc+".."+sendc); if(reader != null) - basesStr = getAllBasesInRegion(reader, sbegc, sendc, basesStr, + basesStr = getAllBasesInRegion(reader, sbegc_raw, sendc_raw, basesStr, features, vcfView, marker.isForwardMarker()); linePos = writeOrView(writer, header, basesStr, buffSeq, linePos); -- GitLab