Shortcut
CharString
A string of char .
Shortcut for
Functions
| Adds a line of text to the help output of the ArgumentParser in the block of ArgParseOptions. | |
| Add list item to ToolDoc object. | |
| Add section to ToolDoc object. | |
| Add the name of a sequence to a GffStream. | |
| Add subsection to ToolDoc object. | |
| Add text line/paragraph to ToolDoc. | |
| Append a new local match to a LocalMatchStore | |
| Appends a name to a name store. | |
| Appends a read to a fragment store. | |
| Extracts the sequence id up to the first whitespace of a sequence file fragment. | |
| Extracts the quality values of a sequence file fragment. | |
| Extracts the quality value id of a sequence file fragment. | |
| Extracts the sequence id of a sequence file fragment. | |
| Assign tags in BAM format to tags in SAM format. | |
| Assign tags in SAM format to tags in BAM format. | |
| Create FaiIndex from FASTA file. | |
| Erase tag from BamTagsDict. | |
| Find a tag by its key for a BamTagsDict object. | |
| Get tool category of ToolDoc object. | |
| Get date string from ToolDoc object. | |
| Get the id/index of a string in a name store with a cache. | |
| Get man title from ToolDoc object. | |
| Get tool name of ToolDoc object. | |
| Get short description of ToolDoc object. | |
| Return tag value from a BamHeaderRecord or BamTagsDict. | |
| Returns a unique name of the current annotation. | |
| Given a key, retrieve its value of the current annotation. | |
| Get version string from ToolDoc object. | |
| Cast from a String-type to a numerical type | |
| Cast from a String-type to a numerical type | |
| Loads contigs into fragment store. | |
| Loads reads into fragment store. | |
| Open a BamStream object for reading/writing. | |
| Parse genomic region string store results in GenomicRegion. | |
| Print ToolDoc object in a given format. | |
| Read characters from stream as long as characters are letters | |
| Read characters from stream as long as characters are digits | |
| Read characters from stream, as long as they are DNA5 characters. Skip over whitespaces. | |
| Read characters from stream as long as the number is a valid floating point numbers. | |
| Read characters from stream as long as characters are graph characters. | |
| Read characters from stream as long as characters are identifiers (alphanumeric, | |
| Read characters from stream as long as characters are letters | |
| Read a line from stream and save it to buffer | |
| Read a line from stream and save it to buffer, remove trailing blanks | |
| Read exactly n characters from stream into buffer | |
| Read n characters from stream into buffer, but skip certain Chars | |
| Read the next sequence record from SequenceStream. | |
| Read characters from stream into buffer until Blank is encountered | |
| Read characters from stream into buffer until Char is encountered | |
| Read characters from stream into buffer until one of the given characters is encountered | |
| Read characters from stream until a tab or line-break occurs. | |
| Read characters from stream into buffer until Whitespace is encountered | |
| Return the name of the sequence with the given id in the FaiIndex. | |
| Set tool category for ToolDoc object. | |
| Set date string for ToolDoc object. | |
| Set version string for ToolDoc object. | |
| Set tool name for ToolDoc object. | |
| Set short description for ToolDoc object. | |
| Set the value of a tag through a BamTagsDict. | |
| Set version string for ToolDoc object. | |
| Write different types to stream | |
| Write a score matrix to a stream. | |
| Write one sequence record from to a SequenceStream object. |
See Also
SeqAn - Sequence Analysis Library - www.seqan.de