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ksahlin
/
strobealign
Aligns short reads using dynamic seed size with strobemers
MIT License
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Get rid of add_to_hits_per_ref() min_diff parameter
#330
marcelm
closed
10 months ago
1
Update README.md
#329
marcelm
closed
10 months ago
1
Rework single-end MAPQ computation
#328
marcelm
closed
7 months ago
7
Avoid MAPQ=60 for single-end multimappers
#327
marcelm
closed
10 months ago
7
Refactoring
#326
marcelm
closed
10 months ago
1
Strobealign gets killed when I try to run/index it
#325
lajoycemboning
closed
11 months ago
3
tmp folder creation
#324
Subhayan18
closed
10 months ago
2
Fix strobemer count statistics
#323
marcelm
closed
12 months ago
1
Running error with strobealign v0.7.1
#322
psj1997
closed
1 year ago
2
Scoring of read pairs on same vs. different chromosome
#321
marcelm
closed
10 months ago
3
Map paired-end reads that overlap each other’s 5' ends
#320
marcelm
opened
1 year ago
2
If R1 and R2 map to same position, treat them as proper pair
#319
marcelm
closed
1 year ago
6
Add `--details` option for showing alignment details
#318
marcelm
closed
1 year ago
5
prioritize properly mapped read pairs.
#317
y9c
closed
1 year ago
19
Add --count option to dumpstrobes command
#316
marcelm
closed
1 year ago
1
Fix incorrect baseline commit hash
#315
marcelm
closed
1 year ago
0
Do not count randstrobes, but estimate their number
#314
marcelm
closed
9 months ago
10
Use xxh64 to hash the s-mer in syncmers
#313
marcelm
closed
1 year ago
5
Various refactorings
#312
marcelm
closed
1 year ago
1
Fix off-by-one error in statistics
#311
marcelm
closed
1 year ago
0
Ensure syncmer and randstrobe iterators yield same no. of items
#310
marcelm
closed
1 year ago
7
Release 0.11.0
#309
marcelm
closed
1 year ago
2
Figure out why no. of randstrobes is not the same as no. of syncmers
#308
marcelm
closed
1 year ago
1
Compute strobemers in parallel
#307
marcelm
closed
1 year ago
12
Make strobealign work with large references
#306
marcelm
closed
1 year ago
12
Large references
#305
marcelm
closed
9 months ago
2
Do not count randstrobes
#304
marcelm
closed
9 months ago
4
Update kseq++ version
#303
marcelm
closed
1 year ago
1
Speed up index generation slightly by forcing inlining of XXH64
#302
marcelm
closed
1 year ago
1
Fail somewhat gracefully for too large references
#301
marcelm
closed
1 year ago
1
Log index statistics in a nicer way
#300
marcelm
closed
1 year ago
4
Some touchups after #278
#299
marcelm
closed
1 year ago
1
To do after merging new hash table memory layout
#298
marcelm
closed
1 year ago
1
Fix: Allocated buffer was not correctly deleted
#297
marcelm
closed
1 year ago
2
Update SSW to v1.2.5
#296
marcelm
closed
1 year ago
3
Backport SSW fix
#295
marcelm
closed
1 year ago
1
`NM` tag might be not calculated correctly in some situation
#294
y9c
closed
1 year ago
4
Reads get MAPQ=60 although they are multimappers
#293
marcelm
closed
10 months ago
5
Document how to make a release
#292
marcelm
closed
1 year ago
1
Set RNAME and POS of unmapped read identical to mate
#291
marcelm
closed
1 year ago
3
Fix secondary alignments not having CIGAR strings
#290
marcelm
closed
1 year ago
3
CIGAR is not recognized by `samtools`
#289
valentynbez
closed
1 year ago
6
Fix invalid QUAL for FASTA input
#288
marcelm
closed
1 year ago
3
SAM QUAL field is incorrect for FASTA input
#287
valentynbez
closed
1 year ago
4
Make rescue_mate more efficient by returning position in `has_shared_substring`?
#286
ksahlin
opened
1 year ago
1
map overflow - large reference db
#285
alejandrorgijon
closed
1 year ago
2
Move v0.7 evaluation section to a separate file
#284
marcelm
closed
1 year ago
1
Refference segments' coordinates probelem
#283
AlAuAu
closed
1 year ago
6
Fix tests to be compatible with MSVC/MinGW
#282
teepean
closed
1 year ago
3
Use string views instead of strings when extracting query randstrobes
#281
althonos
closed
1 year ago
3
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