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Issues list

The possibility of MPI implementation of StrobeAlign feature New feature or request
#14 opened Feb 20, 2022 by jianshu93 updated Mar 11, 2022
Alignment of long reads feature New feature or request
#24 opened Jun 1, 2022 by ksahlin updated Jun 1, 2022
Benchmark writing SAM output and speed it up
#63 opened Sep 9, 2022 by marcelm updated Sep 9, 2022
Consider adding uncompressed BAM as output format
#64 opened Sep 9, 2022 by marcelm updated Sep 9, 2022
Strobealign as reusable library? feature New feature or request
#39 opened Aug 17, 2022 by ksahlin updated Sep 20, 2022
2
Two modes --fast (default) and --sensitive in strobealign? feature New feature or request
#135 opened Nov 1, 2022 by ksahlin updated Nov 2, 2022
Extension alignments longer than 2000 bp
#170 opened Dec 5, 2022 by marcelm updated Dec 5, 2022
Determine whether re-estimating insert size distribution for each chunk changes accuracy
#171 opened Dec 5, 2022 by marcelm updated Dec 7, 2022
@marcelm
1
The index: 32bit hashes instead of 64bit optimization Further information is requested
#27 opened Jun 1, 2022 by ksahlin updated Dec 19, 2022
4
Use of data prefetching?
#203 opened Jan 26, 2023 by jkbonfield updated Jan 26, 2023
3
Run accuracy tests in CI
#218 opened Jan 31, 2023 by marcelm updated Jan 31, 2023
A potential way to save space for genomes smaller than 2^32nt. optimization Further information is requested
#227 opened Feb 5, 2023 by ksahlin updated Feb 8, 2023
6
Base level alignment optimization Further information is requested
#26 opened Jun 1, 2022 by ksahlin updated Feb 8, 2023
3
MAPQ scores feature New feature or request high priority Extra attention is needed
#25 opened Jun 1, 2022 by ksahlin updated Feb 22, 2023
8
Supplementary reads feature New feature or request high priority Extra attention is needed
#13 opened Feb 18, 2022 by kcleal updated Mar 7, 2023
9
Request: executable binary
#253 opened Mar 7, 2023 by Subhayan18 updated Mar 7, 2023
2
Compiling on a M1 Mac bug Something isn't working
#2 opened Nov 22, 2021 by jianshu93 updated Apr 3, 2023
10
Does --interleaved need to support mixed input?
#274 opened Apr 28, 2023 by marcelm updated Apr 28, 2023
2
Additional benchmarks
#276 opened Apr 30, 2023 by ksahlin updated Apr 30, 2023
Make rescue_mate more efficient by returning position in has_shared_substring?
#286 opened Jun 1, 2023 by ksahlin updated Jun 1, 2023
1
Possible issue with mate CIGAR string
#18 opened Feb 24, 2022 by TDDB-limagrain updated Jun 7, 2023
10
Try other syncmer hash functions
#216 opened Jan 30, 2023 by marcelm updated Jun 15, 2023
14
Map paired-end reads that overlap each other’s 5' ends
#320 opened Jun 29, 2023 by marcelm updated Jun 29, 2023
2
Avoid counting the seeds
#340 opened Sep 19, 2023 by marcelm updated Sep 19, 2023
1
Adding smaller biological datasets for mini-benchmarks
#341 opened Sep 19, 2023 by ksahlin updated Sep 19, 2023
ProTip! Exclude everything labeled bug with -label:bug.