v6.1.0

6.1.0 (2024-11-06)

Features

• Add longtr support (#232) (93ff231)
• Add options to facilitate debugging annotaTR runs on large files (#234) (0d5d96b)
• adding the annotaTR tool (#226) (59dd532)
• support for Apple M1 silicon (#227) (dfec9c2)

Bug Fixes

• associatr test files overwritten during pytest (#230) (2b955be)
• bug in beagle dosages with no alt alleles (#231) (ae3ca15)
• enable filter_hrun with beagle file in dumpSTR (be63e79)

Documentation

• generate internal links dynamically (#228) (9402042)
• mention github codespaces and clarify dependency management (#223) (45ccf28)
• update biorxiv citation for prancSTR (#235) (1e45d23)
• warn about scipy deprecation in dumpSTR (#221) (a1a3a39)

v6.0.2

6.0.2 (2024-06-24)

Bug Fixes

• support for numpy 2.0 (#220) (8661226)

Documentation

• update hipstr link (#217) (e1f8511)

v6.0.1

6.0.1 (2024-02-21)

Bug Fixes

• clone command in test_trtools.sh testing script now works in pip installed versions of TRTools (#214) (756a516)

v6.0.0

6.0.0 (2024-02-19)

⚠ BREAKING CHANGES

• remove pybedtools as a dependency. This slightly changes the interpretation of BED files. From now on, the end position of each region will not be included. (#184)
• drop support for python 3.6 and specify unofficial support for python 3.7. Going forward, we will only continue to support versions of python that are "end of life".

Features

• add version constraints, poetry, and poetry.lock file, and use nox-poetry and py3.12 in CI (#202) (ed9c961)

Bug Fixes

• deprecation of binom_test in scipy 1.12.0 and cryptic error occurring with incorrect VCFs in cyvcf2 0.30.26 (#208) (78ec86a)

Code Refactoring

• remove pybedtools as a dependency. This slightly changes the interpretation of BED files. From now on, the end position of each region will not be included. (#184) (89c1dd3)

v5.1.1

Bug fixes:

• Remove stray files from source distribution (#195)

v5.1.0

New features:

• Added prancSTR for mosaicism detection
• Added simTR for simulating NGS reads with stutter errors at TRs

v5.0.2

v5.0.2