rust-bio / rust-bio / 1122
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johanneskoester 
Partial order aligner (#188)

* First commit of work-in-progress branch with a partial-order aligner

* Add updated Cargo file with graph dependency

* Cleaning out POA imports and beginning integration into rust-bio

* fix KMP when pattern is at start of text

* initial commit of read-pair joining

* renaming, broken tests

* update test in doc

* clean up doc

* raise the default min_score (temporary)

* parameterize min_score

* support arbitrary (u8, u8) -> u8 overlap mending functions

* some documentation and tests

* delint

* properly compensate for minimum overlap

* more test cases

* switch to global alignment

* hitting off-by-one for longer queries

* undo previous: off-by-one is in aln.operations

* added template for tests

* massively purge poa module

* begin naive Needleman-Wunsch implementation for graphs

* loud and broken traces

* broken recurrence

* fixed index errors

* NW score is correct, added test case

* Levenshtein distance for graphs with branches

* traceback matrix now stores alignment operation

* construct operation sequence from traceback matrix

* incorporate an alignment (broken)

* incorporate alignment, partially working

* traversal of nodes is reversed in incorporation!!

* start cleaning up

* clear compiler warnings

* remove mating work from master

* read mating stuff moved out of my master branch

* omg

* deletion test case

* some ad hoc test cases

* test for correct edges in incorporation test cases

* temporary: introduce bubbles for mismatches

* increment edge weights instead of making new ones

* update test cases for new incorporation behaviour

* let's fix up the docs

* generalize documentation, rename TracebackCell struct for consistency

* keep test cases in test macros

* fmt

* start of huge, broken refactoring

* fmt

* refactor passes tests

* removed unused imports, API much more consistent... (continued)

7145 of 7777 relevant lines covered (91.87%)

0.92 hits per line

Jobs
ID Job ID Ran Files Coverage
1 1122.1 0
91.87
 Travis Job 1122.1
Source Files on build 1122
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