From: Erik Garrison <erik.garrison@bc.edu>
Date: Wed, 9 Jun 2010 13:39:07 +0000 (-0400)
Subject: fixed potential bug with previous commit
X-Git-Url: https://git.donarmstrong.com/?p=bamtools.git;a=commitdiff_plain;h=c1a31e056e6867ada6f18baaff983f932e8f1177

fixed potential bug with previous commit

The previous commit made assumptions about the ordering of subtags
within @RG header lines.  This commit only assumes that the read group
ID is specified by "ID", thus following spec.
---

diff --git a/BamMultiReader.cpp b/BamMultiReader.cpp
index 58d82a2..92911c9 100644
--- a/BamMultiReader.cpp
+++ b/BamMultiReader.cpp
@@ -237,12 +237,12 @@ const string BamMultiReader::GetHeaderText(void) const {
                 stringstream headerLineSs(headerLine);
                 string part, readGroupPart, readGroup;
                 while(std::getline(headerLineSs, part, '\t')) {
-                    if (part == "@RG") {
-                       std::getline(headerLineSs, readGroupPart, '\t');
-                       stringstream readGroupPartSs(readGroupPart);
-                       std::getline(readGroupPartSs, readGroup, ':');
-                       std::getline(readGroupPartSs, readGroup, ':');
-                       break;
+                    stringstream partSs(part);
+                    string subtag;
+                    std::getline(partSs, subtag, ':');
+                    if (subtag == "ID") {
+                        std::getline(partSs, readGroup, ':');
+                        break;
                     }
                 }
                 if (readGroups.find(readGroup) == readGroups.end()) { // prevents duplicate @RG entries