5f449c5cae
fixed potential integer overflows
2021-07-16 17:20:05 -04:00
b046052d82
Merge branch 'master' into utec
2021-07-16 13:32:47 -04:00
260a68d232
Use #defines for CIGAR operators in C code
...
Give the CIGAR constants names to clarify the code. So that ksw2.h
remains self-contained, define KSW_* versions of the CIGAR operators
it needs for use within ksw2.h. Other code should in general use the
full set of MM_CIGAR_* constants in minimap.h.
2021-07-02 13:03:03 -04:00
177eef259d
Use the full MIDNSHP=X string whenever printing CIGAR strings
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Define MM_CIGAR_STR to the full string of CIGAR operators (including
the 'B' operator as well) and use it throughout the C code.
It would be possible to use it from the Cython code too, but it's easier
to keep that as a Cython string literal to avoid adding extra runtime
code to handle locale conversion.
2021-07-02 13:03:03 -04:00
4f91558160
r1048: rescue long gaps
2021-05-24 16:09:09 -04:00
827ca4b461
r1012: fixed an off-by-one bug; resolves #489
2021-04-07 23:31:31 -04:00
c9874e2dc5
Initialize r->p if ez->zdropped
2020-06-12 09:22:18 -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
a7a01fe5bd
r973: fixed compiling errors caused
2020-01-21 10:43:31 -05:00
eb3ed6993d
support ALT mapping
2020-01-21 09:17:50 -05:00
69af86657e
r935: fixed a cigar like 5I6D7I; resolved #392
2019-04-30 21:35:24 -04:00
be171aa2dc
implemented in exts; testing is the next
2019-04-28 16:47:12 -04:00
cf2bae6e9b
r904: fixed a corner-case segfault. Resolves #307 .
2019-01-10 09:57:05 -05:00
83a8ee7038
r888: fixed incorrect CIGAR when --eqx in use
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This was caused by mm_fix_cigar() which may change query/target offset in very
rare cases. Generating EQX has to beware of this change.
Resolves #266
2018-11-18 14:22:29 -05:00
88c421e8de
r881: a recent change reduces sr accuracy
2018-11-05 22:03:59 -05:00
13981404e2
r876: skip DP if taking too much RAM ( #259 )
2018-11-05 11:43:10 -05:00
377c7099a8
r858: fixed a bug; resolves #254
2018-10-22 22:47:11 -04:00
d04ac068fd
r852: a minor when large --end-bonus is in use
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We may use a large --end-bonus to mimic end-to-end alignment. In the short-read
mode, the candidate alignment region may be out of the band, which leads to
truncated alignment.
2018-10-15 21:28:27 -04:00
5ab6538757
r822: added option --no-end-flt
2018-08-05 19:42:12 -04:00
4b707aac92
working with toy examples
2018-07-15 10:55:00 -04:00
951c0d1d35
apparently mm_append_cigar() wastes some memory
2018-07-14 23:47:44 -04:00
66674afd09
r794: fixed a bug in seed filtering
2018-06-20 10:26:29 -04:00
7e6e8ca73f
r792: fixed -Wextra warnings and resolved #184
2018-06-19 15:26:58 -04:00
3d3bcc29a8
Fix CIGAR reallocation with --eqx
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Fix the logic that calculates the number of CIGAR entries when
match "M" entries are expanded into "=" and "X". The number
of entries depends not on the number of mismatches but rather
on the number of transitions between "=" to "X".
2018-06-19 14:37:41 -04:00
154d2caf5b
r784: support the =/X CIGAR operators ( #156 )
2018-05-30 16:11:22 -04:00
a3afeec0b2
r783: reverted to r781 ( #155 )
2018-05-30 15:25:34 -04:00
9f4309c376
r777: avoid skipping too many seeds
2018-05-11 10:25:18 -04:00
881b4ca3a2
r774: Merge branch 'hot-fix' into fix-long-gap
2018-05-11 10:02:17 -04:00
e61812ee55
reduced gap len to trigger bad seed filtering
2018-05-01 16:17:21 -04:00
734ac379bb
r770: matching N bases not working properly ( #155 )
2018-04-30 19:55:23 -04:00
759f8e4ac9
r769: filter out seeds breaking long gaps
2018-04-24 15:37:37 -04:00
83c57a9d98
r719: fixed bad memory access
2018-02-23 17:27:41 -05:00
a0d62519c1
r710: fixed incorrect inversion coordinate ( #112 )
2018-02-15 14:23:42 -05:00
1372977a37
r708: implemented double Z-drop thresholds ( #112 )
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When aligning long reads, we would prefer to align through low-quality
regions. This requires a large Z-drop threshold. However, to find small
inversions, we need to use a small Z-drop. This commit address this
conflict with two Z-drop thresholds. When Z-drop exceeds the smaller
threshold, we perform a local alignment to check if there is a potential
inversion. If there is one, we break the alignment; otherwise we break
the alignment only if Z-drop excess the larger threshold.
This commit also fixes a bug that reported wrong coordinates when the
inversion is on the forward strand (#112 ).
2018-02-15 10:50:49 -05:00
c0e0d5d84b
r707: bugfix for inversions on rev strand ( #112 )
2018-02-14 14:09:03 -05:00
7ef5490884
r703: added --max-clip-ratio
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still testing the option
2018-02-12 13:29:18 -05:00
a8d476c6ad
r686: end seed trimming don't go over long join
2018-02-06 11:31:32 -05:00
29b4a1786c
r685: tune end seed filter again
2018-02-05 11:48:22 -05:00
dbf284b2d9
r684: separate end score from min_chain_score
2018-02-05 11:40:38 -05:00
35d3e064bf
r677: reduce the change of missing hits
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that are close to end of alignments. It is still possible to create examples
that fail the heuristic.
2018-02-02 10:35:33 -05:00
12a5a5fa3c
r669: improved self chain extension ( #10 )
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This has not fully resolved #10 , only alleviated the issue.
2018-01-30 20:05:02 -05:00
33f8157961
r655: options to map to one strand of the ref #91
2018-01-16 10:34:30 -05:00
f5cfd439ee
r651: incorrectly treat introns as deletions
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This happened when the last operation during backtracking is an intron.
2018-01-07 19:42:50 -05:00
98a6e52c06
r618: heuristics to avoid tiny terminal exons
2017-12-11 00:57:55 -05:00
824712a4ee
r617: removed some unused code
2017-12-10 17:54:50 -05:00
0e42628ef6
r611: document --idx-no-seq; better inv aln
2017-12-08 13:16:18 -05:00
2f463b1db0
r573: prepare to generalize index
2017-11-11 19:54:06 -05:00
d7a31e40e6
r569: last commit is buggy
2017-11-09 23:20:41 -05:00
dd18cd75de
r568: revert - don't take max(dp_max, dp_score)
2017-11-09 23:12:48 -05:00
a7b38f6900
r562: fixed a severe bug: wrong query start
2017-11-08 22:31:05 -05:00
Heng Li
John Marshall
Armin Töpfer
Aaron Wenger