Merge branch 'master' of https://github.com/pezmaster31/bamtools

[bamtools.git] / src / toolkit / bamtools_resolve.cpp

diff --git a/src/toolkit/bamtools_resolve.cpp b/src/toolkit/bamtools_resolve.cpp
index e38ad10d72860f7c59d897ed548ee5903f612789..9e5fb8489d1daaf46fb5abc5404fa143c610f611 100644 (file)
--- a/src/toolkit/bamtools_resolve.cpp
+++ b/src/toolkit/bamtools_resolve.cpp
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // bamtools_resolve.cpp (c) 2011
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 6 July 2011
+// Last modified: 24 July 2013 (DB)
 // ---------------------------------------------------------------------------
 // Resolves paired-end reads (marking the IsProperPair flag as needed).
 // ***************************************************************************
@@ -74,6 +73,20 @@ static const string OPTION_FORCEMARKREADGROUPS  = "ForceMarkReadGroups";
 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
 // --------------------------------------------------------------------------
@@ -732,9 +745,13 @@ void ResolveTool::StatsFileWriter::WriteHeader(void) {
                   << 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;
 }
 
@@ -760,8 +777,8 @@ void ResolveTool::StatsFileWriter::WriteOptions(ResolveTool::ResolveSettings* se
 
     m_stream << OPTIONS_TOKEN << endl
              << OPTION_CONFIDENCEINTERVAL   << EQUAL_CHAR << settings->ConfidenceInterval << endl
-             << OPTION_MINIMUMMAPQUALITY    << EQUAL_CHAR << settings->MinimumMapQuality << endl
              << OPTION_FORCEMARKREADGROUPS  << EQUAL_CHAR << boolalpha << settings->HasForceMarkReadGroups << endl
+             << OPTION_MINIMUMMAPQUALITY    << EQUAL_CHAR << settings->MinimumMapQuality << endl
              << OPTION_UNUSEDMODELTHRESHOLD << EQUAL_CHAR << settings->UnusedModelThreshold << endl
              << endl;
 }