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 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