Trtools

Bug fixes

* MergeSTR now will no longer sometimes emit an alternate allele
identical to the ref allele when dealing with flanking base pairs.

Bug fixes

* Remove outdated call in qcSTR to `np.float()`

Features

* associaTR has been released!

Current limitations:

* Does not support binary phenotypes yet
* Does not support producing data for plotting individual loci yet
* Values in the output file aside from the p-values, coefficients and
standard errors have not been fully tested

Bug fixes

* Fix bioconda build

Features

* TRTools can now read VCFs produced by Beagle imputation.

Bug fixes

* MergeSTR now successfully merges files containing multiple
chromosomes instead of emitting a \'stuck in infinite loop\' message
and crashing
* MergeSTR no longer crashes if run with the \--verbose flag and the
last position in each of the VCFs being merged isn\'t identical.
* StatSTR now errors out if any of the files listed in \--samples
contain no samples that are present in the input VCF.
* DumpSTR now reads call depth from the LC format field when the DP
format field is not present. This was intended previously but was
not happening.

Documentation

* Clarified in PUBLISHING.rst how to handle dependencies and how to
publish to bioconda.
* requirements.txt was unneeded, so delete it and remove the reference
to it from PUBLISHING.rst

Functionality Changes

* MergeSTR: Flanking basepairs are now removed from HipSTR records
before merging. In particular, records with different flank lengths
but the same repeat section will now merge instead of being marked
as incompatible.
* CompareSTR: the tool now only compares records that start and end at
the same position. If a partial overlap in records is detected, the
program will output a warning to the user. This warning contains IDs
of the records and their positions.

Misc

* mergeutils: function GetMinHarmonizedRecords was transformed into
GetIncrementAndComparability, which allows the caller to define
custom predicate that decides whether records are comparable.