From 33add6354f2be9b268450de9002644bd220acf6b Mon Sep 17 00:00:00 2001 From: Erik Garrison Date: Fri, 7 Dec 2012 18:07:55 -0500 Subject: [PATCH] resolve bamtools #68 Check that the quality string is fully comprised of "*", rather than if the first character is "*". --- src/api/internal/bam/BamWriter_p.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/api/internal/bam/BamWriter_p.cpp b/src/api/internal/bam/BamWriter_p.cpp index 1bb086f..637bb7a 100644 --- a/src/api/internal/bam/BamWriter_p.cpp +++ b/src/api/internal/bam/BamWriter_p.cpp @@ -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[0] == '*' || al.Qualities[0] == (char)0xFF ) + if ( al.Qualities.empty() || ( al.Qualities.size() == 1 && 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