Heng Li 51cfb60520 r145: changed default -p from 2 to 0.8 ...

For long reads, secondary alignments can be very information.

2017-07-02 22:51:45 -04:00

.gitignore

make sdust working with kalloc

2017-04-06 15:51:36 -04:00

align.c

r126: filter by fraction of seed coverage

2017-06-30 22:15:45 -04:00

bseq.c

r131: wrong EOF test; make mb_size <= batch_size

2017-07-01 09:26:09 -04:00

bseq.h

r129: fixed memory leak caused by qualities

2017-06-30 23:48:00 -04:00

chain.c

finished the first draft of manpage

2017-07-01 11:25:54 -04:00

format.c

r121: output QUAL and unmapped to SAM

2017-06-30 14:40:54 -04:00

hit.c

r144: adjust primary aln after cigar

2017-07-02 22:43:02 -04:00

index.c

r131: wrong EOF test; make mb_size <= batch_size

2017-07-01 09:26:09 -04:00

kalloc.c

number of allocated units must be an even number

2017-06-26 23:15:30 -04:00

kalloc.h

Homopolymer-compressed k-mer sketch

2017-04-06 15:37:34 -04:00

kdq.h

make sdust working with kalloc

2017-04-06 15:51:36 -04:00

khash.h

index can be compiled; not tested yet

2017-04-07 15:30:30 -04:00

kseq.h

Homopolymer-compressed k-mer sketch

2017-04-06 15:37:34 -04:00

ksort.h

chaining

2017-05-03 20:47:29 +08:00

ksw2_extz2_sse.c

backup

2017-06-29 12:58:52 -04:00

ksw2.h

backup

2017-06-29 12:58:52 -04:00

kthread.c

index can be compiled; not tested yet

2017-04-07 15:30:30 -04:00

kthread.h

index can be compiled; not tested yet

2017-04-07 15:30:30 -04:00

kvec.h

Homopolymer-compressed k-mer sketch

2017-04-06 15:37:34 -04:00

LICENSE.txt

added license

2017-07-01 11:39:19 -04:00

main.c

r145: changed default -p from 2 to 0.8

2017-07-02 22:51:45 -04:00

Makefile

code refactoring for mm_reg1_t

2017-06-29 19:35:38 -04:00

map.c

r145: changed default -p from 2 to 0.8

2017-07-02 22:51:45 -04:00

minimap2.1

r145: changed default -p from 2 to 0.8

2017-07-02 22:51:45 -04:00

minimap.h

r144: adjust primary aln after cigar

2017-07-02 22:43:02 -04:00

misc.c

sort positions in each bucket

2017-04-12 13:31:12 -04:00

mmpriv.h

fixed bug when retaining 2ndary aln; still buggy

2017-07-02 19:08:30 -04:00

sdust.c

fixed memory leaks

2017-06-06 21:45:55 -04:00

sdust.h

fixed a few memory leaks

2017-04-13 23:05:19 -04:00

sketch.c

wrong HPC

2017-05-04 17:45:19 +08:00

Description

A versatile pairwise aligner for genomic and spliced nucleotide sequences

bioinformaticsgenomicssequence-alignmentspliced-alignment

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