Shortcut
CharString
A string of char.
This is a useful replacement of std::string. If you want a C-style char * string, use toCString.
CharString
Shortcut for
String<char, Alloc<> >
Functions
addLineAdds a line of text to the help output of the ArgumentParser in the block of ArgParseOptions.
addListItemAdd list item to ToolDoc object. Appends a list item to the ArgumentParser.
addSectionAdd section to ToolDoc object. Begins a new section of ArgParseOption the help output of the ArgumentParser.
addSubSectionAdd subsection to ToolDoc object.
addTextAdd text line/paragraph to ToolDoc. Appends a text paragraph to the ArgumentParser.
appendLocalMatchAppend a new local match to a LocalMatchStore
appendNameAppends a name to a name store.
appendReadAppends a read to a fragment store.
assignCroppedSeqIdExtracts the sequence id up to the first whitespace of a sequence file fragment.
assignQualExtracts the quality values of a sequence file fragment.
assignQualIdExtracts the quality value id of a sequence file fragment.
assignSeqIdExtracts the sequence id of a sequence file fragment.
assignTagsBamToSamAssign tags in BAM format to tags in SAM format.
assignTagsSamToBamAssign tags in SAM format to tags in BAM format.
buildCreate FaiIndex from FASTA file.
databaseNameReference to the name (identifier) of the database in a Blast report.
eraseTagErase tag from BamTagsDict.
findTagKeyFind a tag's key of a BamHeaderRecord.
getCategoryGet tool category of ToolDoc object. Get tool category of ArgumentParser object.
getDatabaseNameThe name (identifier) of the database in a Blast report.
getDateGet date string from ToolDoc object.
getIdByNameAppends a name to a name store.
getManTitleGet man title from ToolDoc object.
getNameGet tool name of ToolDoc object.
getQueryNameThe name (identifier) of the query in a Blast report.
getShortDescriptionGet short description of ToolDoc object. Gets short description of ArgumentParser.
getTagValueReturn tag value from a BamHeaderRecord or BamTagsDict.
getUniqueNameReturns a unique name of the current annotation.
getValueByKeyGiven a key, retrieve its value of the current annotation.
getVersionGet version string from ToolDoc object. Get version string from ArgumentParser object.
lexicalCastCast from a String-type to a numerical type
lexicalCast2Cast from a String-type to a numerical type
loadContigsLoads contigs into fragment store.
loadReadsLoads reads into fragment store.
openOpen a BamStream object for reading/writing.
parseParse genomic region string store results in GenomicRegion.
printPrint ToolDoc object in a given format.
queryNameReference to the name (identifier) of the query in a Blast report.
readAlphaNumsRead characters from stream as long as characters are letters
readDigitsRead characters from stream as long as characters are digits
readDna5IgnoringWhitespacesRead characters from stream, as long as they are DNA5 characters. Skip over whitespaces.
readFloatRead characters from stream as long as the number is a valid floating point numbers.
readGraphsRead characters from stream as long as characters are graph characters.
readIdentifierRead characters from stream as long as characters are identifiers (alphanumeric, '-', and '_').
readLettersRead characters from stream as long as characters are letters
readLineRead a line from stream and save it to buffer
readLineStripTrailingBlanksRead a line from stream and save it to buffer, remove trailing blanks
readNCharsRead exactly n characters from stream into buffer
readNCharsIgnoringWhitespaceRead n characters from stream into buffer, but skip certain Chars
readRecordRead the next sequence record from SequenceStream. Read the next sequence record from SequenceStream.
readUntilBlankRead characters from stream into buffer until Blank is encountered
readUntilCharRead characters from stream into buffer until Char is encountered
readUntilOneOfRead characters from stream into buffer until one of the given characters is encountered
readUntilTabOrLineBreakRead characters from stream until a tab or line-break occurs.
readUntilWhitespaceRead characters from stream into buffer until Whitespace is encountered
sequenceNameReturn the name of the sequence with the given id in the FaiIndex.
setCategorySet tool category for ToolDoc object. Set tool category for ArgumentParser object.
setDateSet date string for ToolDoc object. Sets date string of ArgumentParser.
setManTitleSet version string for ToolDoc object.
setNameSet tool name for ToolDoc object.
setShortDescriptionSet short description for ToolDoc object. Sets short description of the ArgumentParser object.
setTagValueSet the value of a tag through a BamTagsDict.
setVersionSet version string for ToolDoc object. Sets version string of ArgumentParser.
streamPutWrite different types to stream
write 
writeRecordWrite one sequence record from to a SequenceStream object.
See Also
SeqAn - Sequence Analysis Library - www.seqan.de
 

Page built @2012/10/02 11:10:36