X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Ftoolkit%2Fbamtools_split.cpp;h=e6602a9e590e250d3dd204fea990db579db20db4;hb=e7d0ca0a024a13d405872be90f381ff397cdaeec;hp=4575d8596cc9c1dc8b808e8690f3ca2bfbb2d08d;hpb=72f5b82ad353b4cc9d6f8153f1ad19cc387b9597;p=bamtools.git

diff --git a/src/toolkit/bamtools_split.cpp b/src/toolkit/bamtools_split.cpp
index 4575d85..e6602a9 100644
--- a/src/toolkit/bamtools_split.cpp
+++ b/src/toolkit/bamtools_split.cpp
@@ -2,7 +2,7 @@
 // bamtools_split.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 7 April 2011 (DB)
+// Last modified: 8 December 2011 (DB)
 // ---------------------------------------------------------------------------
 // Splits a BAM file on user-specified property, creating a new BAM output
 // file for each value found
@@ -69,6 +69,7 @@ struct SplitTool::SplitSettings {
     // flags
     bool HasInputFilename;
     bool HasCustomOutputStub;
+    bool HasCustomRefPrefix;
     bool IsSplittingMapped;
     bool IsSplittingPaired;
     bool IsSplittingReference;
@@ -76,6 +77,7 @@ struct SplitTool::SplitSettings {
     
     // string args
     string CustomOutputStub;
+    string CustomRefPrefix;
     string InputFilename;
     string TagToSplit;
     
@@ -83,11 +85,13 @@ struct SplitTool::SplitSettings {
     SplitSettings(void)
         : HasInputFilename(false)
         , HasCustomOutputStub(false)
+        , HasCustomRefPrefix(false)
         , IsSplittingMapped(false)
         , IsSplittingPaired(false)
         , IsSplittingReference(false)
         , IsSplittingTag(false)
         , CustomOutputStub("")
+        , CustomRefPrefix("")
         , InputFilename(Options::StandardIn())
         , TagToSplit("")
     { } 
@@ -298,6 +302,16 @@ bool SplitTool::SplitToolPrivate::SplitReference(void) {
     map<int32_t, BamWriter*> outputFiles;
     map<int32_t, BamWriter*>::iterator writerIter;
     
+    // determine reference prefix
+    string refPrefix = SPLIT_REFERENCE_TOKEN;
+    if ( m_settings->HasCustomRefPrefix )
+        refPrefix = m_settings->CustomRefPrefix;
+
+    // make sure prefix starts with '.'
+    const size_t dotFound = refPrefix.find('.');
+    if ( dotFound != 0 )
+        refPrefix = string(".") + refPrefix;
+
     // iterate through alignments
     BamAlignment al;
     BamWriter* writer;
@@ -311,9 +325,17 @@ bool SplitTool::SplitToolPrivate::SplitReference(void) {
         // if no writer associated with this value
         if ( writerIter == outputFiles.end() ) {
         
+            // fetch reference name for ID
+            string refName;
+            if ( currentRefId == -1 )
+                refName = "unmapped";
+            else
+                refName = m_references.at(currentRefId).RefName;
+
+            // construct new output filename
+            const string outputFilename = m_outputFilenameStub + refPrefix + refName + ".bam";
+
             // open new BamWriter
-            const string refName = m_references.at(currentRefId).RefName;
-            const string outputFilename = m_outputFilenameStub + SPLIT_REFERENCE_TOKEN + refName + ".bam";
             writer = new BamWriter;
             if ( !writer->Open(outputFilename, m_header, m_references) ) {
                 cerr << "bamtools split ERROR: could not open " << outputFilename
@@ -373,9 +395,13 @@ bool SplitTool::SplitToolPrivate::SplitTag(void) {
             case (Constants::BAM_TAG_TYPE_STRING) :
             case (Constants::BAM_TAG_TYPE_HEX)    :
                 return SplitTagImpl<string>(al);
+
+            case (Constants::BAM_TAG_TYPE_ARRAY) :
+                cerr << "bamtools split ERROR: array tag types are not supported" << endl;
+                return false;
           
             default:
-                fprintf(stderr, "bamtools split ERROR: unknown tag type encountered: [%c]\n", tagType);
+                cerr << "bamtools split ERROR: unknown tag type encountered: " << tagType << endl;
                 return false;
         }
     }
@@ -506,12 +532,18 @@ SplitTool::SplitTool(void)
     , m_impl(0)
 {
     // set program details
-    Options::SetProgramInfo("bamtools split", "splits a BAM file on user-specified property, creating a new BAM output file for each value found", "[-in <filename>] [-stub <filename stub>] < -mapped | -paired | -reference | -tag <TAG> > ");
+    const string name = "bamtools split";
+    const string description = "splits a BAM file on user-specified property, creating a new BAM output file for each value found";
+    const string args = "[-in <filename>] [-stub <filename stub>] < -mapped | -paired | -reference [-refPrefix <prefix>] | -tag <TAG> > ";
+    Options::SetProgramInfo(name, description, args);
     
     // set up options 
     OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
     Options::AddValueOption("-in",   "BAM filename",  "the input BAM file",  "", m_settings->HasInputFilename,  m_settings->InputFilename,  IO_Opts, Options::StandardIn());
-    Options::AddValueOption("-stub", "filename stub", "prefix stub for output BAM files (default behavior is to use input filename, without .bam extension, as stub). If input is stdin and no stub provided, a timestamp is generated as the stub.", "", m_settings->HasCustomOutputStub, m_settings->CustomOutputStub, IO_Opts);
+    Options::AddValueOption("-refPrefix", "string", "custom prefix for splitting by references. Currently files end with REF_<refName>.bam. This option allows you to replace \"REF_\" with a prefix of your choosing.", "",
+                            m_settings->HasCustomRefPrefix, m_settings->CustomRefPrefix, IO_Opts);
+    Options::AddValueOption("-stub", "filename stub", "prefix stub for output BAM files (default behavior is to use input filename, without .bam extension, as stub). If input is stdin and no stub provided, a timestamp is generated as the stub.", "",
+                            m_settings->HasCustomOutputStub, m_settings->CustomOutputStub, IO_Opts);
     
     OptionGroup* SplitOpts = Options::CreateOptionGroup("Split Options");
     Options::AddOption("-mapped",    "split mapped/unmapped alignments",       m_settings->IsSplittingMapped,    SplitOpts);