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69 Commits

Author SHA1 Message Date
Heng Li
3187782b1a r1285: better --spsc support 2025-05-26 15:47:14 -04:00
Heng Li
819b3bf017 r1274: a little better pass-1 
Also fixed a bug in jump
 2025-04-13 13:55:15 -04:00
Heng Li
e88110463a r1273: reading pass1 junctions works 
but we need extra logic when using them. Tomorrow.
 2025-04-13 00:47:28 -04:00
Heng Li
fb81e150f2 r1272: support pass-1 junction processing 
NOT tested yet
 2025-04-12 23:15:04 -04:00
Heng Li
d930ea94ad r1271: code refactoring in prep for 2-pass 2025-04-11 17:20:34 -04:00
Heng Li
2ed264db4e r1257: fixed the sorting of BED files 2025-04-06 10:53:16 -04:00
Heng Li
9ede5c4255 backup 2025-04-06 00:07:15 -04:00
Heng Li
a8c567b5e9 r1251: read junctions for jumps 2025-04-04 16:23:19 -04:00
Heng Li
d9d3c0cc3f refactored --junc-bed 2025-04-03 21:02:50 -04:00
Heng Li
cbe8d61ca4 r1249: remove redundant junctions in --junc-bed 2025-04-03 20:43:06 -04:00
Heng Li
54fa925e2e r1240: fixed wrong logging information 
resolve #1192
 2025-04-01 09:17:39 -04:00
Heng Li
68179ed195 r1215: scoring apparently works 2024-10-12 22:29:27 -04:00
Heng Li
e4e1f7843b backup for spsc 2024-10-10 22:43:50 -04:00
blawrence-ont
f3e59fc2a0 Avoid NULL pointer dereference (#1154) 
If the allocated region is 0 bytes then it's unsafe to dereference it.

Fixes #1147.
 2024-01-24 12:32:05 -05:00
Heng Li
4483f89ee5 Release minimap2-2.25 (r1173) 2023-04-25 12:44:52 -04:00
Heng Li
c2f07ff2ac r1149: implemented random open syncmer 
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
Heng Li
b046052d82 Merge branch 'master' into utec 2021-07-16 13:32:47 -04:00
Heng Li
2b47846cd6 r1008: don't parse space in BED 2021-04-05 11:41:00 -04:00
Heng Li
da7109fd29 r985: optionally report cs/cg on the query strand 
PAF only; not well tested
 2020-04-21 12:37:35 -04:00
Heng Li
eb3ed6993d support ALT mapping 2020-01-21 09:17:50 -05:00
Heng Li
47b646acbf r961: print indexed length 2020-01-06 21:13:33 -05:00
Heng Li
49c6d83a8e r934: --junc-bed to read BED12 2019-04-28 20:12:28 -04:00
Heng Li
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
Heng Li
f4c844b143 fixed a few simple bugs and leaks 2019-04-28 16:47:12 -04:00
Heng Li
be171aa2dc implemented in exts; testing is the next 2019-04-28 16:47:12 -04:00
Heng Li
6420acca6d BED I/O 2019-04-28 16:47:12 -04:00
Heng Li
b0f39a1a61 r823: mappy to index a single sequence 2018-08-05 20:57:05 -04:00
Mark Bicknell
8c064a5f29 Fixed mm_idx_is_idx to return the correct result on Windows. 2018-07-17 09:16:33 -04:00
Heng Li
395c8d678a r815: fixed a memory leak 2018-07-15 22:11:32 -04:00
Heng Li
1a55227d5a write hits to tmp files (unfinished) 2018-07-14 12:15:10 -04:00
Heng Li
7e6e8ca73f r792: fixed -Wextra warnings and resolved #184 2018-06-19 15:26:58 -04:00
Ilya Kolpakov
408e098859 fix deserialization of zero-length reference names 2018-06-19 14:46:05 -04:00
Ilya Kolpakov
4c66b689c3 fix serialization of empty names in mm_idx_dump 2018-06-19 14:46:05 -04:00
Heng Li
24a4808826 r718: retrieve sequence from the index 2018-02-23 10:18:26 -05:00
Heng Li
543fa12e68 r659: for C++ compatibility 2018-01-19 10:40:18 -05:00
Heng Li
e420b17496 r629: API to construct index from strings 2017-12-18 22:29:46 -05:00
Heng Li
fec7bd713f r610: warning if db sequence is 0-lengthed (#69) 2017-12-07 21:05:39 -05:00
Heng Li
131cfc6938 r574: build index without sequences 2017-11-11 21:38:38 -05:00
Heng Li
2f463b1db0 r573: prepare to generalize index 2017-11-11 19:54:06 -05:00
Heng Li
afc2f2e84b r536: removed an unnecessary assert() 2017-10-24 21:08:54 -04:00
Heng Li
4f6244bd4a revamped README; not finished yet 2017-10-06 13:02:25 -04:00
Heng Li
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
Heng Li
84bbc47152 two arrays should be freed with kfree(0,) 
though in the current code, they are strictly equivalent.
 2017-09-23 10:43:22 -04:00
Heng Li
5966e5d6e4 make reader_open() work even if idxopt is NULL 2017-09-15 11:29:49 -04:00
Heng Li
e2823d4aee r367: index reader optionally writes index 2017-09-14 21:18:13 -04:00
Heng Li
eb00521d9b redesigned indexing and option APIs 2017-09-14 17:02:01 -04:00
Heng Li
3c91d652dd r360: allow to set integer max occ 2017-09-13 11:37:00 -04:00
Heng Li
0a3ebdc916 for better windows compatibility 2017-09-02 17:52:33 -04:00
Stefan von Deylen
a3c3db6b9b ONT source code changes to compile with MSVC 14 2017-08-30 16:25:20 +01:00
Heng Li
0fe1a224ab r309: improved SAM header output 2017-08-25 10:35:58 +08:00