From c5363861478f495b41a2ad99028326f85feeb905 Mon Sep 17 00:00:00 2001 From: derek Date: Wed, 17 Nov 2010 19:41:29 -0500 Subject: [PATCH] Changed GetNextAlignmentCore() calls to GetNextAlignment() in FilterTool --- src/toolkit/bamtools_filter.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/toolkit/bamtools_filter.cpp b/src/toolkit/bamtools_filter.cpp index 83f67ac..d2de3b4 100644 --- a/src/toolkit/bamtools_filter.cpp +++ b/src/toolkit/bamtools_filter.cpp @@ -3,7 +3,7 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 4 October 2010 +// Last modified: 17 November 2010 // --------------------------------------------------------------------------- // Filters BAM file(s) according to some user-specified criteria. // *************************************************************************** @@ -793,7 +793,7 @@ bool FilterTool::FilterToolPrivate::Run(void) { } // everything checks out, just iterate through specified region, filtering alignments - while ( reader.GetNextAlignmentCore(al) ) + while ( reader.GetNextAlignment(al) ) if ( CheckAlignment(al) ) writer.SaveAlignment(al); } @@ -801,7 +801,7 @@ bool FilterTool::FilterToolPrivate::Run(void) { // no index data available, we have to iterate through until we // find overlapping alignments else { - while ( reader.GetNextAlignmentCore(al) ) { + while ( reader.GetNextAlignment(al) ) { if ( (al.RefID >= region.LeftRefID) && ((al.Position + al.Length) >= region.LeftPosition) && (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) ) { -- 2.39.2