rust-bio / rust-bio / 775
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johanneskoester 
banded Smith-Waterman (#104)

* sparse dp: LCSk++

* docs and example

* fix doc test

* use generics to accept more types of inputs

* fix tests

* switch to QGram index for finding matches. move BitTree to it's own file, and fix up docs

* better help about find_kmer_matches

* return a struct, add more docs

* get qgram matches directly without extending

* move find_kmer_matches to sparse.

* banded sw, using band calculated w/ sparse dp

* clean up docs & remove println!

* for one-off alignment, use the simpler kmer matcher

* wip banded

* working banded sw
- added generalized LCSk++ that has gap penalties
- refactored alignment::pairwise slightly to let normal and banded SW coexist

* remove println

* use faster find_kmer_matches

* test for global aln issue

* test + fix for global alignments w/ trailing indels

* turn off printing of traceback matrices inside alignment

* Implemented Smith-Waterman alignment with clipping penalty.

* As suggested by FrancisRussell, this commit rewrites the matrix traceback code so it's stored as a single vector.

* Ran rustfmt

* Code simplification and many minor optimizations.

* Added code for Banded Smith Waterman Aligner for all alignment modes.

* Changed the implementation of Scoring struct, which now uses a MatchFunc
trait instead of a reference to std:ops::Fn. This makes the struct self-contained
and gives the flexibility of being passed around and returned from Functions.

* Minor bug correction in assert. Added test case for the new scoring function and a bunch of documentation

* More documentation for the trait MatchFunc

* Added Debug, Clone traits for MatchParams

* Minor change: Added Clone trait to Alignment struct

* WIP

* Added fn to create bam cigar from alignment, with a bunch of test cases. The function relies on the external dependency rust_htslib

* The traceback matrix is cleared in the init fn.  Without this the initital values are not set correctly when reusing the same aligner for different alignment.
Reduced the MAX_CELLS to 1e5.

* Added custom_with_matches which accepts a sorted kmer match and computed the alignment (no hashing)

* report correct length of local alignments

* add accessors for alignment length and some comments

* ylen and xlen are the lengths of the original sequences

* larger size max array size for banded alignment.  the the sparse DP know the match and gap penalties

* remove print

* inline the score function of MatchFunc

* Bug fix: when the banded alignment ends outside the band due to clipping, choose between indel/clipping to reach  the origin instead of only clipping

* For computing gap penalty in sdpkpp, instead of Manhattan distance, use the maximum distance along x or y. Added a new fn expand_matches() which extends the match skeleton tolerating a user specified number of mismatches

* Banded aligner supports expanded matches and union with lcskpp path

* Rustfmt

* Update .gitignore

* update copyright to reflect authors of bit_tree.rs

* generalize FenwickTree impl, remove Alignment --> Cigar converter: will move to rust-htslib

* unneeded method in qgram

5562 of 6024 relevant lines covered (92.33%)

2.72 hits per line

Jobs
ID Job ID Ran Files Coverage
1 775.1 0
92.25
 Travis Job 775.1
2 775.2 0
96.32
 Travis Job 775.2
3 775.3 0
96.32
 Travis Job 775.3
Source Files on build 775
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