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
Alloc String
String<char, Alloc<> >
Functions

addLine | Adds a line of text to the help output of the ArgumentParser in the block of ArgParseOptions.
addListItem | Add list item to ToolDoc object.
addSection | Add section to ToolDoc object.
addSequenceName | Add the name of a sequence to a GffStream.
addSubSection | Add subsection to ToolDoc object.
addText | Add text line/paragraph to ToolDoc.
appendLocalMatch | Append a new local match to a LocalMatchStore
appendName | Appends a name to a name store.
appendRead | Appends a read to a fragment store.
assignCroppedSeqId | Extracts the sequence id up to the first whitespace of a sequence file fragment.
assignQual | Extracts the quality values of a sequence file fragment.
assignQualId | Extracts the quality value id of a sequence file fragment.
assignSeqId | Extracts the sequence id of a sequence file fragment.
assignTagsBamToSam | Assign tags in BAM format to tags in SAM format.
assignTagsSamToBam | Assign tags in SAM format to tags in BAM format.
build | Create FaiIndex from FASTA file.
eraseTag | Erase tag from BamTagsDict.
findTagKey | Find a tag by its key for a BamTagsDict object.
getCategory | Get tool category of ToolDoc object.
getDate | Get date string from ToolDoc object.
getIdByName | Get the id/index of a string in a name store with a cache.
getManTitle | Get man title from ToolDoc object.
getName | Get tool name of ToolDoc object.
getShortDescription | Get short description of ToolDoc object.
getTagValue | Return tag value from a BamHeaderRecord or BamTagsDict.
getUniqueName | Returns a unique name of the current annotation.
getValueByKey | Given a key, retrieve its value of the current annotation.
getVersion | Get version string from ToolDoc object.
lexicalCast | Cast from a String-type to a numerical type
lexicalCast2 | Cast from a String-type to a numerical type
loadContigs | Loads contigs into fragment store.
loadReads | Loads reads into fragment store.
open | Open a BamStream object for reading/writing.
parse | Parse genomic region string store results in GenomicRegion.
print | Print ToolDoc object in a given format.
readAlphaNums | Read characters from stream as long as characters are letters
readDigits | Read characters from stream as long as characters are digits
readDna5IgnoringWhitespaces | Read characters from stream, as long as they are DNA5 characters. Skip over whitespaces.
readFloat | Read characters from stream as long as the number is a valid floating point numbers.
readGraphs | Read characters from stream as long as characters are graph characters.
readIdentifier | Read characters from stream as long as characters are identifiers (alphanumeric, '-', and '_').
readLetters | Read characters from stream as long as characters are letters
readLine | Read a line from stream and save it to buffer
readLineStripTrailingBlanks | Read a line from stream and save it to buffer, remove trailing blanks
readNChars | Read exactly n characters from stream into buffer
readNCharsIgnoringWhitespace | Read n characters from stream into buffer, but skip certain Chars
readRecord | Read the next sequence record from SequenceStream.
readUntilBlank | Read characters from stream into buffer until Blank is encountered
readUntilChar | Read characters from stream into buffer until Char is encountered
readUntilOneOf | Read characters from stream into buffer until one of the given characters is encountered
readUntilTabOrLineBreak | Read characters from stream until a tab or line-break occurs.
readUntilWhitespace | Read characters from stream into buffer until Whitespace is encountered
sequenceName | Return the name of the sequence with the given id in the FaiIndex.
setCategory | Set tool category for ToolDoc object.
setDate | Set date string for ToolDoc object.
setManTitle | Set version string for ToolDoc object.
setName | Set tool name for ToolDoc object.
setShortDescription | Set short description for ToolDoc object.
setTagValue | Set the value of a tag through a BamTagsDict.
setVersion | Set version string for ToolDoc object.
streamPut | Write different types to stream
write | Write a score matrix to a stream.
writeRecord | Write one sequence record from to a SequenceStream object.

See Also
CharIterator
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2014/10/13 16:12:59