biocommons / hgvs / 308
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Closes #437: Optionally allow out-of-bounds transcript variation (#590)

* added docker-compose file and updated README

* started CIGARMapper (incomplete)

* incorporated alignmentmapper into cigarmapper module for testing/comparison

* more cleanup of new cigarmapper and comparisons

* initial migration of alignmentmapper to cigarmapper; some tests still fail

* added mapper.strict_transcript_bounds option to config

* streamlined test_hgvs_alignmentmapper to facilitate comparison (in future commits)

* checkpoint of non-functional code; changing strategy

* alignmentmapper.py → alignmentmapper_new.py

* alignmentmapper_old.py → alignmentmapper.py

* tests pass again

* Factored CIGARMapper out of AlignmentMapper (take 2); tests pass!

* untangled AlignmentMapper's use of private data and methods

* moved CIGARMapper to separate module; tests pass

* removed alignmentmapper_new.py

* renamed mapping arg `base` to `end`

* moved parse_cigar to alignmentmapper

* added cigarmapper tests

* rename parse_cigar to _parse_cigar

* added strict_bounds flag to cigarmapper (default=True; not yet in alignmentmapper)

* added new strict_bounds flag to alignment mapper methods, with default from global_config

* added tests for issue 437 (and they pass!)

* removed unnecessary validation check

* rename legacy r_{start,end} to n_{start,end} for consistency elsewhere

* minor test rearrangement

* update cigarmapper test alignment docs for clarity about intent

* fixed recently introduced bug that considered last base of transcript as out-of-bounds

* fixed bug caused by test data missing from cache, inexplicably

* adding more missing data from cache

* fixed incorrect test of 3' terminus

* rename 437 tests

* removed alignmentmapper exception tests that no longer apply

* support negative n. coordinates

* reworked #437 tests to use fixtures to speed up tests

* verified and reenabled test fo... (continued)

2156 of 2334 relevant lines covered (92.37%)

1.85 hits per line

Jobs
ID Job ID Ran Files Coverage
1 308.1 0
92.37
 Travis Job 308.1
2 308.2 0
92.37
 Travis Job 308.2
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