| Interface | Description |
|---|---|
| PETags |
Basic interface for holding sets of sequence tag (these are compressed into 2-bit codings of tags). The length of tag in good sequence is also tracked.
|
| Reads |
Basic methods for working with nextgen reads
|
| RepGenData | |
| RepGenDataWriter | |
| Tag |
Interface for tags (sequences without N) that captures these bit encoded sequence and there length.
|
| TagData |
Interface to GBS Tag Data. Replaces TagsCounts, TBT, and TOPM TODO: TAS-476
|
| TagDataWriter |
Defines writer to modify the GBS tag data store
|
| Tags |
Basic interface for holding sets of sequence tag (these are compressed into 2-bit codings of tags). The length of tag in good sequence is also tracked.
|
| TagsByTaxa |
Tags by Taxa is the interface for tracking the distribution of tags across taxa. It can be thought of as a matrix of nTaxa by nTags. Taxa names are also maintained by this interface.
|
| TaxaDistribution |
This is a specialized multiset for recording the distribution of a single across taxa. HashMap or Multiset or large arrays could be reasonable approaches by they do not scale well with hundreds of taxa scored out of the thousands. Instead this the general implementations use primitive arrays.
|
| Class | Description |
|---|---|
| AbstractPETags |
Basic methods for working with PE Tags, including sorting and search.
|
| AbstractTag |
Created by edbuckler on 7/26/14.
|
| AbstractTags |
Basic methods for working with Tags, including sorting and search.
|
| AbstractTagsByTaxa |
Basic method implementation of Tags by Taxa, including methods for reading and writing files
|
| AbstractTagsHDF5 |
Basic implementations of HDF5 tags. This is designed to annotate tags with a bunch of attributes, to solve the memory issues
|
| FastqReader | |
| GBSHDF5Constants |
Path definitions for the HDF5 GBS file formats.
|
| PETagCounts |
Hold PE tags and their counts, also including contigs
|
| ReadsByTaxa | |
| RepGenSQLite | |
| SAMUtils | |
| TagBuilder |
Builder for tags that optimizes the memory footprint. Tags are encoded in long with 2 bits per bp. In GBS, we generally use only record the 64 or 96bp. Custom classes are generated with 32, 64 or 96bp tags (1, 2 or 3 longs) otherwise an array is used.
|
| TagCountMutable |
Resizeable tags count container. Tags sequences are compressed in long, tags lengths are tracked, and read counts are stored. Has basic filtering methods. Read counts can be modified.
|
| TagCounts |
Holds tags counts. Tags sequences are compressed in long, tags lengths are tracked, and read counts are stored. Has basic filtering methods. Read counts can be modified. This class is not resizable in terms of new tags - for growing tag count lists use TagCountMutable.java User: ed
|
| TagDataSQLite |
Defines xxxx TAS-480
|
| TagsByTaxaByte |
A bit implementation of TagByTaxa, so only counts as high as 127 can be maintained.
|
| TagsByTaxaByteFileMap |
A byte implementation of TagByTaxa, maximum depth of tags is 127. This version works directly from a RandomAccessFile, which is slow but can work with very large files. It will need to be transitioned nio2, when Java 7 comes out. If possible, it holds the current row cached in memory, so try to work with the files sequentially.
|
| TagsByTaxaByteFileMapSeq |
A bit implementation of TagByTaxa, so only presence or absence of a tags is known. This version works directly from a RandomAccessFile, which is slow but can work with very large files. It will need to be transitioned nio2, when Java 7 comes out. If possible, it holds the current row cached in memory, so try to work with the files sequentially.
|
| TagsByTaxaByteHDF5TagGroups |
Tags by Taxa file based on the HDF5 data structure. This version is optimized for rapid access of taxa within Tag (ie it buffers the taxa counts within one tag).
|
| TagsByTaxaByteHDF5TaxaGroups |
Tags by Taxa file based on the HDF5 data structure. This version is optimized for rapid access of tags within taxa (ie it buffers the tag counts within one taxon). It is good for adding, removing, and combining taxa
|
| TagsByTaxaShort |
Tags by taxa that supports depths captured by a short (max 32767)
|
| TagsByTaxaUtils |
This class contains methods which process TagsByTaxa files one line at a time, as opposed to the methods in
|
| TaxaDistBuilder |
Builder for TaxaDistribution. Deals with the
|
| UTagCountMutable | |
| UTagPairs |