- Support for VCFv4.0, which should be identical to 3.3 support
- Correctly handle chromosome references when they start with 'chr' (instead of just numbers)
- Handle extra empty tabs on the header line which are present in GATK produced VCF and confuse the determination of how many sample states should be parsed.
configured at the application level. Specific tabular data files are
specified in a application config file and bound to names, the tools
then refer to these names. Thus users can configure where location
files are located without modifying tool configs.
Also:
- Simpler column name configuration
- Columns can be referred to by name in addition to index in all
dynamic option filters
- A data table can merge multiple files
- Design can support other types of data files
This file should be used for display purposes only (e.g as a UCSC Custom Track). Performing an analysis using the output created by this tool as input is not recommended; the source VCF file should be used when performing an analysis.
Unknown nucleotides are represented as '*' as required to allow the display to draw properly; these include e.g. reference bases which appear before a deletion and are not available without querying the original reference sequence.
These changes should only affect output when an input block has a species appearing more than once, with the exception being the MAF to multiple FASTA blocks converters: the FASTA headers have been revised to included the sequence index for a species in a block as well as the block index.
A new tool "Split MAF Blocks by Species" has been added that will split MAF blocks into the complete combination of multiple blocks when a species appears more than once.
Allow most MAF tools to allow limiting of output species. MAF tools which do not allow species limiting include Extract Pairwise MAF blocks, MAF Coverage stats, and Filter MAF blocks by Size.
The functionality of Filter MAF blocks by Species and Filter MAF blocks by Size is now available in Filter MAF by specified attributes. Unfortunately tests are still not able to be written for the Filter MAF by specified attributes tool.
These are now used to store the list of chromosomes for species as well as the index for MAF files.
MAF tools have been enhanced to make use of index files when available.
TODO: When datasets are purged from disk, these files should also be purged.
permissions, user-side permissions settings on datasets, viewing
associated datasets under the role page in the admin controler (is this
even necessary?), filtering out roles by type. I haven't addressed
tests, so the security-related functional tests will fail. I haven't
looked at history sharing yet either. Cleanup to remove unused methods
is needed in the admin controller. And the admin templates are a
bit messy.
Nicola Soranzo