c2f07ff2ac
r1149: implemented random open syncmer
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On the mm2-update dataset, -j8 leads to sparser k-mer selection at higher
accuracy. The speed becomes a little slower. There seems a benefit but not a
big one.
2022-10-21 19:07:28 -04:00
b046052d82
Merge branch 'master' into utec
2021-07-16 13:32:47 -04:00
2b47846cd6
r1008: don't parse space in BED
2021-04-05 11:41:00 -04:00
da7109fd29
r985: optionally report cs/cg on the query strand
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PAF only; not well tested
2020-04-21 12:37:35 -04:00
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
47b646acbf
r961: print indexed length
2020-01-06 21:13:33 -05:00
49c6d83a8e
r934: --junc-bed to read BED12
2019-04-28 20:12:28 -04:00
e80759c97a
--junc-bed apparently working
...
Also fixed an issue with splice alignment in the reverse strand, though this
should have a very minor effect in practice.
2019-04-28 16:47:12 -04:00
f4c844b143
fixed a few simple bugs and leaks
2019-04-28 16:47:12 -04:00
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
6420acca6d
BED I/O
2019-04-28 16:47:12 -04:00
b0f39a1a61
r823: mappy to index a single sequence
2018-08-05 20:57:05 -04:00
8c064a5f29
Fixed mm_idx_is_idx to return the correct result on Windows.
2018-07-17 09:16:33 -04:00
395c8d678a
r815: fixed a memory leak
2018-07-15 22:11:32 -04:00
1a55227d5a
write hits to tmp files (unfinished)
2018-07-14 12:15:10 -04:00
7e6e8ca73f
r792: fixed -Wextra warnings and resolved #184
2018-06-19 15:26:58 -04:00
408e098859
fix deserialization of zero-length reference names
2018-06-19 14:46:05 -04:00
4c66b689c3
fix serialization of empty names in mm_idx_dump
2018-06-19 14:46:05 -04:00
24a4808826
r718: retrieve sequence from the index
2018-02-23 10:18:26 -05:00
543fa12e68
r659: for C++ compatibility
2018-01-19 10:40:18 -05:00
e420b17496
r629: API to construct index from strings
2017-12-18 22:29:46 -05:00
fec7bd713f
r610: warning if db sequence is 0-lengthed ( #69 )
2017-12-07 21:05:39 -05:00
131cfc6938
r574: build index without sequences
2017-11-11 21:38:38 -05:00
2f463b1db0
r573: prepare to generalize index
2017-11-11 19:54:06 -05:00
afc2f2e84b
r536: removed an unnecessary assert()
2017-10-24 21:08:54 -04:00
4f6244bd4a
revamped README; not finished yet
2017-10-06 13:02:25 -04:00
7d50e646dd
r466: detect multi-part index more smartly
...
though it might not work in an extremely rare case: the end of a sequence ends
at X*16384 and it is the last sequence in a batch. This can be resolved by
never letting the kstream_t buffer empty.
2017-10-04 17:32:58 -04:00
84bbc47152
two arrays should be freed with kfree(0,)
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though in the current code, they are strictly equivalent.
2017-09-23 10:43:22 -04:00
5966e5d6e4
make reader_open() work even if idxopt is NULL
2017-09-15 11:29:49 -04:00
e2823d4aee
r367: index reader optionally writes index
2017-09-14 21:18:13 -04:00
eb00521d9b
redesigned indexing and option APIs
2017-09-14 17:02:01 -04:00
3c91d652dd
r360: allow to set integer max occ
2017-09-13 11:37:00 -04:00
0a3ebdc916
for better windows compatibility
2017-09-02 17:52:33 -04:00
a3c3db6b9b
ONT source code changes to compile with MSVC 14
2017-08-30 16:25:20 +01:00
0fe1a224ab
r309: improved SAM header output
2017-08-25 10:35:58 +08:00
f81f37fef1
r197: allocate index seq names from kalloc
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to reduce malloc() overhead.
2017-07-24 19:36:05 -04:00
5c4d040b13
r191: warning if CLI index opt diff from prebuilt
...
Also added index testing API (moved from main.c to index.c)
2017-07-19 10:25:11 -04:00
71c988f6ab
r188: renamed bseq* to mm_bseq*
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to avoid naming collisions between minimap2 and bwa/fermi-lite/etc
2017-07-19 09:26:46 -04:00
a9f089f0aa
r131: wrong EOF test; make mb_size <= batch_size
2017-07-01 09:26:09 -04:00
41efd03d7a
r129: fixed memory leak caused by qualities
2017-06-30 23:48:00 -04:00
de54c9dac2
r77: fixed an index loading bug (offset not set)
2017-06-26 13:56:25 -04:00
44cdd18de0
start to work on alignment
2017-06-23 13:44:45 -04:00
d816e48fce
fixed a bug in chaining
2017-06-06 14:33:43 -04:00
6d4348db44
dp chaining mostly works, but fails sometimes
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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
949d9be872
chaining with DP
2017-05-09 22:20:57 +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
56723ad580
moved `sum_len` out of the index
...
as it can be inferred.
2017-04-19 11:06:24 -04:00
f35e152e99
fixed a few memory leaks
2017-04-13 23:05:19 -04:00
Heng Li
Mark Bicknell
Ilya Kolpakov
Stefan von Deylen