// bamtools_resolve.cpp (c) 2011
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 12 October 2011
+// Last modified: 24 July 2013 (DB)
// ---------------------------------------------------------------------------
// Resolves paired-end reads (marking the IsProperPair flag as needed).
// ***************************************************************************
static const string RG_FIELD_DESCRIPTION =
"#<name> <medianFL> <minFL> <maxFL> <topModelID> <nextTopModelID> <isAmbiguous?>";
+static const string MODEL_DESCRIPTION =
+ "# ------------- Model Types Description ---------------\n"
+ "#\n"
+ "# ID Position Orientation \n"
+ "# 1 mate1 < mate2 mate1:forward, mate2:forward \n"
+ "# 2 mate1 < mate2 mate1:forward, mate2:reverse \n"
+ "# 3 mate1 < mate2 mate1:reverse, mate2:forward \n"
+ "# 4 mate1 < mate2 mate1:reverse, mate2:reverse \n"
+ "# 5 mate2 < mate1 mate2:forward, mate1:forward \n"
+ "# 6 mate2 < mate1 mate2:forward, mate1:reverse \n"
+ "# 7 mate2 < mate1 mate2:reverse, mate1:forward \n"
+ "# 8 mate2 < mate1 mate2:reverse, mate1:reverse \n"
+ "# -----------------------------------------------------\n";
+
// --------------------------------------------------------------------------
// unique readname file constants
// --------------------------------------------------------------------------
<< BAMTOOLS_VERSION_BUILD;
// # bamtools resolve (vX.Y.Z)
+ // #
+ // # MODEL DESCRIPTION - see above for actual text
// \n
m_stream << COMMENT_CHAR << " bamtools resolve (" << versionStream.str() << ")" << endl
+ << COMMENT_CHAR << endl
+ << MODEL_DESCRIPTION
<< endl;
}
SamReadGroupConstIterator rgIter = header.ReadGroups.ConstBegin();
SamReadGroupConstIterator rgEnd = header.ReadGroups.ConstEnd();
for ( ; rgIter != rgEnd; ++rgIter ) {
- const SamReadGroup& rg = rgIter->second;
+ const SamReadGroup& rg = (*rgIter);
m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) );
}
}