From a645ad57edeec989e753a4414aa0bdbfb0854077 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 12 Jul 2012 11:56:55 +0100
Subject: [PATCH] fix for creating features from read peaks with concat
sequences
---
.../artemis/components/alignment/BamUtils.java | 3 ++-
.../artemis/components/alignment/MappedReads.java | 15 +++++++++++++--
2 files changed, 15 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamUtils.java b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
index 8ad6da6ce..84e90f524 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
@@ -166,6 +166,7 @@ class BamUtils
final String refName,
final int start,
final int end,
+ final int concatShift,
final int cnt[][],
final SAMRecordPredicate samRecordFlagPredicate,
final SAMRecordPredicate samRecordMapQPredicate)
@@ -194,7 +195,7 @@ class BamUtils
int refStart = block.getReferenceStart();
for(int i=0; i<block.getLength(); i++)
{
- int pos = refStart + i;
+ int pos = refStart + i + concatShift;
int bin = pos - start;
if(bin < 0 || bin > cnt.length-1)
continue;
diff --git a/uk/ac/sanger/artemis/components/alignment/MappedReads.java b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
index f065b85bb..230f26e0b 100644
--- a/uk/ac/sanger/artemis/components/alignment/MappedReads.java
+++ b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
@@ -487,9 +487,20 @@ public class MappedReads
if( (start >= offset && start <= offset+len) ||
(stop >= offset && start <= offset+len) )
{
+ int thisStart = start-offset;
+ if(thisStart < 1)
+ thisStart = 1;
+ int thisEnd = stop-offset;
+ if(thisEnd > len)
+ thisEnd = len;
+
+ int concatShift = 0;
+ if(offset > start)
+ concatShift = offset-start;
+
cnt =
BamUtils.countOverRange(bamList.get(i), samFileReaderHash,
- name, start-offset, stop-offset, cnt,
+ name, thisStart, thisEnd, concatShift, cnt,
samRecordFlagPredicate, samRecordMapQPredicate);
}
}
@@ -498,7 +509,7 @@ public class MappedReads
{
cnt =
BamUtils.countOverRange(bamList.get(i), samFileReaderHash,
- refSeq, start, stop, cnt,
+ refSeq, start, stop, 0, cnt,
samRecordFlagPredicate, samRecordMapQPredicate);
}
--
GitLab