From 08df4771c832c3fea1837edf39fa082e233d33c2 Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 30 Jun 2009 16:08:55 +0000 Subject: [PATCH] count X/N/etc. as mismatches for the NM attribute in the BAMs git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1127 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/playground/indels/AlignmentUtils.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java b/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java index df1eb3749..3f8cc2adb 100644 --- a/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java +++ b/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java @@ -135,9 +135,10 @@ public class AlignmentUtils { continue; char refChr = refSeq.charAt(refIndex); char readChr = readSeq.charAt(readIdx); - if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 || - BaseUtils.simpleBaseToBaseIndex(refChr) == -1 ) - continue; // do not count Ns/Xs/etc ? + // Note: we need to count X/N's as mismatches because that's what SAM requires + //if ( BaseUtils.simpleBaseToBaseIndex(readChr) == -1 || + // BaseUtils.simpleBaseToBaseIndex(refChr) == -1 ) + // continue; // do not count Ns/Xs/etc ? if ( Character.toUpperCase(readChr) != Character.toUpperCase(refChr) ) mismatches++; }