From a3fe14aec4988a0db1da9011195c3bc71b5223d6 Mon Sep 17 00:00:00 2001 From: Derek Barnett Date: Sun, 18 Nov 2012 23:55:53 -0500 Subject: [PATCH] Fixed: BamWriter behavior on missing quality string (0xFF) * See Issue #65 --- src/api/internal/bam/BamWriter_p.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/api/internal/bam/BamWriter_p.cpp b/src/api/internal/bam/BamWriter_p.cpp index 8877800..1bb086f 100644 --- a/src/api/internal/bam/BamWriter_p.cpp +++ b/src/api/internal/bam/BamWriter_p.cpp @@ -2,7 +2,7 @@ // BamWriter_p.cpp (c) 2010 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 4 April 2012 (DB) +// Last modified: 18 November 2012 (DB) // --------------------------------------------------------------------------- // Provides the basic functionality for producing BAM files // *************************************************************************** @@ -284,7 +284,7 @@ void BamWriterPrivate::WriteAlignment(const BamAlignment& al) { // write the base qualities char* pBaseQualities = new char[queryLength](); - if ( al.Qualities.empty() || al.Qualities == "*" ) + if ( al.Qualities.empty() || al.Qualities[0] == '*' || al.Qualities[0] == (char)0xFF ) memset(pBaseQualities, 0xFF, queryLength); // if missing or '*', fill with invalid qual else { for ( size_t i = 0; i < queryLength; ++i ) -- 2.39.2