59c822b722
removed some commented code
...
which *might* return at some time later
2017-09-09 08:38:39 -04:00
f422175e4e
r344: avoid unnecessary refName retrieval
2017-09-08 22:44:14 -04:00
101b8bb97d
r335: report an error if query can't be opened
2017-09-03 11:54:38 -04:00
0fe1a224ab
r309: improved SAM header output
2017-08-25 10:35:58 +08:00
993a2bb521
r301: separate introns from deletions
...
When an intron is adjacent to a deletion, the old code count both as introns,
which lead to an inaccurate exon boundary.
2017-08-18 15:31:15 +08:00
64c1389e1a
Merge branch 'master' into splice
2017-08-17 23:39:27 +08:00
bbb37d95f2
support inserting RG lines
2017-08-17 23:34:09 +08:00
2cde8d257c
r297: bidirectional RNA alignment
2017-08-17 06:02:44 -04:00
d240318741
r287: refined CLI options and manpage
2017-08-12 12:26:04 -04:00
0f4c823b0c
r286: ignore introns when computing max seg score
2017-08-12 10:58:16 -04:00
c59b0781bc
r280: output introns as "N" in the cdna mode
2017-08-09 11:45:02 -04:00
1a7d782131
r273: cdna mapping mode for testing
...
Differences from the typical mapping mode:
* banded alignment disabled
* log gap cost during chaining
* zero long-gap extension during alignment
* up to 100kb (by default) reference gap
* bad seeding not filtered (to tune later)
2017-08-08 11:31:49 -04:00
4c0713ee14
r235: optionally output tag cs in PAF
...
cs encodes the query, the reference sequence and CIGAR.
2017-07-31 12:06:49 -04:00
19d6ec885e
r224: inversion alignment around Z-drop break
2017-07-29 13:09:10 -04:00
2179e9e24b
r221: output SA in the SAM output
2017-07-28 23:08:39 -04:00
254280b8af
r216: a bit cleanup; identical output to r215
2017-07-28 11:54:18 -04:00
b927838495
r212: better heuristic to fix wrong seeding
...
but not good enough. Will explore more.
2017-07-27 11:24:51 -04:00
e9dc1ce2b6
r205: when computing mapq, consider min_chain_sc
...
Not doing this was a mistake.
2017-07-26 11:34:14 -04:00
00c6db5073
r203: check more subopt aln if score small
2017-07-25 20:02:44 -04:00
71c988f6ab
r188: renamed bseq* to mm_bseq*
...
to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
2017-07-19 09:26:46 -04:00
71e2a97a4c
r180: changed -x asm5 settings
2017-07-18 00:00:36 -04:00
b4280d186f
r176: removed seedcov_ratio; changed default opt
...
min_seedcov_ratio is not used
2017-07-12 12:47:46 -04:00
52caf79395
r175: halved max-chain-skip in the ava mode
2017-07-12 10:42:19 -04:00
eeeb2ffb68
r174: make max-chain-skip work
...
The max-chain-skip heuristics did not work due to a bug. Without this
heuristics, chaining is too slow for long-read overlap.
2017-07-12 10:08:06 -04:00
33451aba45
r173: changed the debugging output format
2017-07-11 15:23:28 -04:00
826c8ba892
r170: added a debugging flag
...
something wrong with chaining
2017-07-11 14:47:35 -04:00
1ac48556ae
r167: long join threshold depends on gap
...
also caught a bug for reverse strand join
2017-07-09 10:38:51 -04:00
42846ce65d
r163: reduced long join score requirement
...
because the chaining score is generally smaller with the last few commits.
2017-07-08 15:51:52 -04:00
38b2830e18
r161: filter bad seeds; changed default -g/-r
2017-07-08 13:31:27 -04:00
cc554aee43
r159: use two-piece gap penalty
2017-07-08 10:26:00 -04:00
9823317e8f
r158: optionally ignore base quality
2017-07-05 18:23:50 -04:00
e07daad7ad
r153: sam primary record not set sometimes
2017-07-03 13:18:57 -04:00
b625247300
r150: mm_sync_regs() doesn't work with negative id
2017-07-03 11:36:34 -04:00
53c4bf5e4f
r149: introduced debugging flags on CLI
2017-07-03 11:02:32 -04:00
2e4fd9f1d0
r148: revamped regs handling after cigar
2017-07-03 10:44:26 -04:00
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
74d306a596
fixed bug when retaining 2ndary aln; still buggy
2017-07-02 19:08:30 -04:00
41efd03d7a
r129: fixed memory leak caused by qualities
2017-06-30 23:48:00 -04:00
426c2975f6
r126: filter by fraction of seed coverage
...
otherwise we may get too many poor overlap mappings.
2017-06-30 22:15:45 -04:00
646a746cdc
r122: filter contained aln after DP extension
2017-06-30 15:23:30 -04:00
fce87ce7bd
r121: output QUAL and unmapped to SAM
2017-06-30 14:40:54 -04:00
d11049eb32
r120: use max-scoring seg to control output
...
much better now
2017-06-30 14:21:44 -04:00
1a903486b9
r118: bugfix - regs unsorted before filtering
2017-06-30 12:52:28 -04:00
03267e8fa7
r113: fixed a sam header bug
2017-06-29 22:43:06 -04:00
3825feeeac
r111: changed the default z-drop to 200
2017-06-29 21:37:56 -04:00
08cbb09fcc
r109: changed the default scoring
2017-06-29 20:21:57 -04:00
4cd456b9ba
r108: refactoring, move reg1 routines to hit.c
2017-06-29 19:44:11 -04:00
ecedfe5788
code refactoring for mm_reg1_t
2017-06-29 19:35:38 -04:00
cc67f1b781
compute mapq; not working for z-split yet
2017-06-29 17:52:48 -04:00
b9075d39a8
r104: long gap patching
2017-06-29 14:54:54 -04:00
17944a75c2
merge into map.c
2017-06-29 14:20:14 -04:00
c8d122bcdb
backup
2017-06-29 11:11:15 -04:00
9fbf7e41e1
r99: report progress
2017-06-28 23:56:33 -04:00
b696d5fe5e
disable kalloc in the debugging mode
2017-06-28 10:50:27 -04:00
bcd9b1c621
r93: fixed various small issues
2017-06-28 10:35:21 -04:00
cdc2a1e29f
r92: fixed a bug for overlapping alignment
...
On the PBcR example E. coli reads, miniasm gives one circular unitig.
2017-06-27 22:03:31 -04:00
533150d49d
r90: revert default band width to 1000
...
10000 is excessively tolerant with bad hits.
2017-06-27 20:29:39 -04:00
fa80177e58
r89: added minimal number of minimizer counts
2017-06-27 18:43:15 -04:00
99c57b86c5
r79: drop bad hits
2017-06-26 15:28:04 -04:00
5b614ae828
r78: fixed a split bug
2017-06-26 14:45:23 -04:00
de54c9dac2
r77: fixed an index loading bug (offset not set)
2017-06-26 13:56:25 -04:00
640b1a1727
command-line option to control CIGAR output
2017-06-26 11:41:09 -04:00
b1077ff14c
sam output
2017-06-25 22:05:20 -04:00
39083be9ab
separated formating printing
...
for SAM in future; and for performance
2017-06-25 16:13:54 -04:00
f20d550a59
fixed the NM bug
...
due to reversed CIGAR
2017-06-25 11:24:39 -04:00
ef5dd318ca
implemented chain splitting; NOT tested!!!
2017-06-24 22:57:43 -04:00
aa5881e7bb
backup
2017-06-24 22:51:31 -04:00
2d8fda9586
an alternative strategy to fix for HPC
...
it makes the result better, but still not quite right.
2017-06-24 09:26:24 -04:00
0c274280ae
output the original score
2017-06-23 22:56:50 -04:00
2987be288c
output cigar
2017-06-23 22:53:47 -04:00
35b84f88c6
backup
2017-06-23 22:42:15 -04:00
d75b5b4e8a
backup; NOT working yet
2017-06-23 19:21:47 -04:00
990f7b0b71
backup
2017-06-23 15:13:53 -04:00
4ae0b46972
min_ksw_len
2017-06-23 14:38:28 -04:00
44cdd18de0
start to work on alignment
2017-06-23 13:44:45 -04:00
372698bb23
disable k-mer intersection for now
...
My current focus is long-read mapping. This functionality is not needed right now.
2017-06-11 14:13:41 -04:00
b04e4b9215
r36: bring back primary; don't output all mappings
2017-06-08 15:28:19 -04:00
6c099bef89
removed some debugging code
...
not necessary when we can print PAF
2017-06-07 14:49:11 -04:00
be9a7f4e41
removed the old print code
2017-06-07 14:24:31 -04:00
8ad5cfde42
output PAF
2017-06-07 14:18:32 -04:00
c01f2dd757
fixed a bug
2017-06-07 11:40:13 -04:00
c1c946aa67
fixed memory leaks
...
though some of them are not really leaks when kalloc is in use.
2017-06-06 21:45:55 -04:00
e6adb673f9
fixed a stupid bug
2017-06-06 15:45:42 -04:00
a2958a4836
minor tweaks
2017-06-06 15:31:21 -04:00
6d4348db44
dp chaining mostly works, but fails sometimes
...
which means there are bugs that need to be fixed
2017-06-06 14:19:50 -04:00
1a9fc04cf0
backup
2017-06-06 10:16:33 -04:00
acc7382a30
backup
2017-06-04 16:09:45 -04:00
949d9be872
chaining with DP
2017-05-09 22:20:57 +08:00
2827c29b48
minor backup
2017-05-04 23:22:11 +08:00
10db6b0434
wrong HPC
2017-05-04 17:45:19 +08:00
06adabd0dc
clean bill from valgrind
2017-05-04 12:44:49 +08:00
7b53f7aa84
chaining
2017-05-03 20:47:29 +08:00
f2ae8eb670
mostly debugging code
2017-05-01 16:50:09 +08:00
2c9f1bce3e
k-mer thinning apparently working
2017-04-28 18:24:45 +08:00
7b7fabef4d
added idx_stat
2017-04-26 22:52:28 +08:00
de367a340c
compilable again
2017-04-26 19:36:46 +08:00
1bf3ae6752
backup
2017-04-09 15:09:39 -04:00
79c9478f46
backup
2017-04-09 14:59:39 -04:00
8c230563cc
can be compiled
2017-04-07 15:56:10 -04:00
Heng Li