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added list-tag support to bamtools split
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@pezmaster31
pezmaster31 committed Jun 30, 2016
1 parent 6da5c39 commit 8d6d7fc
Showing 1 changed file with 118 additions and 19 deletions.
137 changes: 118 additions & 19 deletions src/toolkit/bamtools_split.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -72,6 +72,7 @@ struct SplitTool::SplitSettings {
bool HasCustomOutputStub;
bool HasCustomRefPrefix;
bool HasCustomTagPrefix;
bool HasListTagDelimiter;
bool IsSplittingMapped;
bool IsSplittingPaired;
bool IsSplittingReference;
Expand All @@ -83,13 +84,15 @@ struct SplitTool::SplitSettings {
string CustomTagPrefix;
string InputFilename;
string TagToSplit;
string ListTagDelimiter;

// constructor
SplitSettings(void)
: HasInputFilename(false)
, HasCustomOutputStub(false)
, HasCustomRefPrefix(false)
, HasCustomTagPrefix(false)
, HasListTagDelimiter(false)
, IsSplittingMapped(false)
, IsSplittingPaired(false)
, IsSplittingReference(false)
Expand All @@ -99,6 +102,7 @@ struct SplitTool::SplitSettings {
, CustomTagPrefix("")
, InputFilename(Options::StandardIn())
, TagToSplit("")
, ListTagDelimiter("--")
{ }
};

Expand Down Expand Up @@ -139,8 +143,14 @@ class SplitTool::SplitToolPrivate {
// finds first alignment and calls corresponding SplitTagImpl<>
// depending on tag type
bool SplitTag(void);
// templated split tag implementation
// handle the various types that are possible for tags

public:

// handles list-type tags
template<typename T>
bool SplitListTagImpl(BamAlignment& al);

// handles single-value tags
template<typename T>
bool SplitTagImpl(BamAlignment& al);

Expand Down Expand Up @@ -383,27 +393,37 @@ bool SplitTool::SplitToolPrivate::SplitTag(void) {
// pass it the current alignment found
switch ( tagType ) {

case (Constants::BAM_TAG_TYPE_INT8) :
case (Constants::BAM_TAG_TYPE_INT16) :
case (Constants::BAM_TAG_TYPE_INT32) :
return SplitTagImpl<int32_t>(al);

case (Constants::BAM_TAG_TYPE_UINT8) :
case (Constants::BAM_TAG_TYPE_UINT16) :
case (Constants::BAM_TAG_TYPE_UINT32) :
return SplitTagImpl<uint32_t>(al);

case (Constants::BAM_TAG_TYPE_FLOAT) :
return SplitTagImpl<float>(al);
case (Constants::BAM_TAG_TYPE_INT8) : return SplitTagImpl<int8_t>(al);
case (Constants::BAM_TAG_TYPE_INT16) : return SplitTagImpl<int16_t>(al);
case (Constants::BAM_TAG_TYPE_INT32) : return SplitTagImpl<int32_t>(al);
case (Constants::BAM_TAG_TYPE_UINT8) : return SplitTagImpl<uint8_t>(al);
case (Constants::BAM_TAG_TYPE_UINT16) : return SplitTagImpl<uint16_t>(al);
case (Constants::BAM_TAG_TYPE_UINT32) : return SplitTagImpl<uint32_t>(al);
case (Constants::BAM_TAG_TYPE_FLOAT) : return SplitTagImpl<float>(al);

case (Constants::BAM_TAG_TYPE_ASCII) :
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;
case (Constants::BAM_TAG_TYPE_ARRAY) : {

char arrayTagType(0);
if (!al.GetArrayTagType(m_settings->TagToSplit, arrayTagType))
continue;
switch(arrayTagType) {
case (Constants::BAM_TAG_TYPE_INT8) : return SplitListTagImpl<int8_t>(al);
case (Constants::BAM_TAG_TYPE_INT16) : return SplitListTagImpl<int16_t>(al);
case (Constants::BAM_TAG_TYPE_INT32) : return SplitListTagImpl<int32_t>(al);
case (Constants::BAM_TAG_TYPE_UINT8) : return SplitListTagImpl<uint8_t>(al);
case (Constants::BAM_TAG_TYPE_UINT16) : return SplitListTagImpl<uint16_t>(al);
case (Constants::BAM_TAG_TYPE_UINT32) : return SplitListTagImpl<uint32_t>(al);
case (Constants::BAM_TAG_TYPE_FLOAT) : return SplitListTagImpl<float>(al);
default:
cerr << "bamtools split ERROR: array tag has unsupported element type: " << arrayTagType << endl;
return false;
}
}

default:
cerr << "bamtools split ERROR: unknown tag type encountered: " << tagType << endl;
Expand Down Expand Up @@ -447,7 +467,83 @@ void SplitTool::SplitToolPrivate::CloseWriters(map<T, BamWriter*>& writers) {
writers.clear();
}

// handle the various types that are possible for tags
// handle list-type tags
template<typename T>
bool SplitTool::SplitToolPrivate::SplitListTagImpl(BamAlignment& al) {

typedef T TagElementType;
typedef vector<T> TagValueType;
typedef map<string, BamWriter*> WriterMap;
typedef typename WriterMap::iterator WriterMapIterator;

// set up splitting data structure
WriterMap outputFiles;
WriterMapIterator writerIter;

// determine tag prefix
string tagPrefix = SPLIT_TAG_TOKEN;
if ( m_settings->HasCustomTagPrefix )
tagPrefix = m_settings->CustomTagPrefix;

// make sure prefix starts with '.'
const size_t dotFound = tagPrefix.find('.');
if ( dotFound != 0 )
tagPrefix = string(".") + tagPrefix;

const string tag = m_settings->TagToSplit;
BamWriter* writer;
TagValueType currentValue;
while (m_reader.GetNextAlignment(al)) {

string listTagLabel;
if (!al.GetTag(tag, currentValue))
listTagLabel = "none";
else {
// make list label from tag data
stringstream listTagLabelStream;
typename TagValueType::const_iterator tagValueIter = currentValue.cbegin();
typename TagValueType::const_iterator tagValueEnd = currentValue.cend();
for (; tagValueIter != tagValueEnd; ++tagValueIter)
listTagLabelStream << (*tagValueIter) << m_settings->ListTagDelimiter;
listTagLabel = listTagLabelStream.str();
if (!listTagLabel.empty())
listTagLabel = listTagLabel.substr(0, listTagLabel.size() - m_settings->ListTagDelimiter.size()); // pop last delimiter
}

// lookup writer for label
writerIter = outputFiles.find(listTagLabel);

// if not found, create one
if (writerIter == outputFiles.cend()) {

// open new BamWriter, save first alignment
stringstream outputFilenameStream;
outputFilenameStream << m_outputFilenameStub << tagPrefix << tag << "_" << listTagLabel << ".bam";
writer = new BamWriter;
if ( !writer->Open(outputFilenameStream.str(), m_header, m_references) ) {
cerr << "bamtools split ERROR: could not open " << outputFilenameStream.str()
<< " for writing." << endl;
return false;
}

// store in map
outputFiles.insert( make_pair(listTagLabel, writer) );
}

// else grab existing writer
else writer = (*writerIter).second;

// store alignment in proper BAM output file
if ( writer )
writer->SaveAlignment(al);
}

// clean up & return success
CloseWriters(outputFiles);
return true;
}

// handle the single-value tags
template<typename T>
bool SplitTool::SplitToolPrivate::SplitTagImpl(BamAlignment& al) {

Expand Down Expand Up @@ -554,13 +650,16 @@ SplitTool::SplitTool(void)

// 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("-in", "BAM filename", "the input BAM file", "",
m_settings->HasInputFilename, m_settings->InputFilename, IO_Opts, Options::StandardIn());
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("-tagPrefix", "string", "custom prefix for splitting by tags. Current files end with TAG_<tagname>_<tagvalue>.bam. This option allows you to replace \"TAG_\" with a prefix of your choosing.", "",
m_settings->HasCustomTagPrefix, m_settings->CustomTagPrefix, 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);
Options::AddValueOption("-tagListDelim", "string", "delimiter used to separate values in the filenames generated from splitting on list-type tags [--]", "",
m_settings->HasListTagDelimiter, m_settings->ListTagDelimiter, IO_Opts);

OptionGroup* SplitOpts = Options::CreateOptionGroup("Split Options");
Options::AddOption("-mapped", "split mapped/unmapped alignments", m_settings->IsSplittingMapped, SplitOpts);
Expand Down

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