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Issues list

segfault using --score-N option for ambiguous nucleotide score
#1226 opened Jun 28, 2024 by nrizzo updated Jun 28, 2024
Mapping 2 wheat genomes
#1115 opened Sep 8, 2023 by mfruzan updated Jun 20, 2024
1
MD string for second reads bug
#226 opened Sep 5, 2018 by hirokiuedaRcast updated Jun 18, 2024
1
1
Allow any nucleotide to map to a specific location question
#973 opened Oct 20, 2022 by meng-lab updated May 24, 2024
7
Documentation: Limitations "small exons" question
#948 opened Aug 3, 2022 by husamia updated May 6, 2024
4
[mappy] DP alignment score in Alignment objects
#1202 opened Apr 26, 2024 by tomdstanton updated Apr 28, 2024
Question about different mappings of same read
#1200 opened Apr 24, 2024 by nadjano updated Apr 24, 2024
mapping HiFi reads using .mmi generated with -x map-ont
#1196 opened Apr 19, 2024 by Geil625 updated Apr 19, 2024
trying to understand the samtools flagstat file after alignment with minimap2
#1193 opened Apr 15, 2024 by sparthib updated Apr 15, 2024
distinct minimizer count integer overflow with large reference fasta
#1192 opened Apr 14, 2024 by cjprybol updated Apr 14, 2024
radix_sort_128x() produces unstable sorting output
#1191 opened Apr 12, 2024 by gsc74 updated Apr 12, 2024
Mappy segfault with long sequence and MD=True bug
#1183 opened Mar 25, 2024 by davidnewman02 updated Mar 27, 2024
2
High memory use when using Python and threads help wanted
#855 opened Jan 5, 2022 by cjw85 updated Mar 14, 2024
10
Cigar issue with no M or N between two I's remains in minimap2 v2.26
#1090 opened Jul 26, 2023 by mebbert updated Mar 4, 2024
9
bug? hit.c:210: mm_hit_sort: Assertion `has_cigar + no_cigar == 1' failed.
#1067 opened May 26, 2023 by dgordon562 updated Jan 4, 2024
1
Chaining score contributions from anchors seem to be capped by the anchor length, but the paper doesn't explain why question
#1125 opened Oct 24, 2023 by adamnovak updated Nov 9, 2023
2
Order of operations in CIGAR enhancement
#1118 opened Sep 27, 2023 by baraaorabi updated Nov 3, 2023
4
Command usage .
#1120 opened Oct 12, 2023 by dvirdi01 updated Oct 12, 2023
How to solve logic inconsistency?
#1084 opened Jul 9, 2023 by Keltonc updated Sep 13, 2023
1
Reference Weirdness
#1113 opened Sep 6, 2023 by jonathan-bravo updated Sep 6, 2023
making clips more favourable than matching (and reducing secondary mappings)
#1112 opened Sep 1, 2023 by kcajj updated Sep 6, 2023
Potential duplicate generation of RG tag on inputs with RG information
#1110 opened Aug 30, 2023 by SHuang-Broad updated Aug 30, 2023
zd flag in paf in field 22 shared with rl
#1108 opened Aug 24, 2023 by gchevignon updated Aug 24, 2023
Question regarding aligning two fastq files
#1105 opened Aug 18, 2023 by Le1223 updated Aug 21, 2023
1
Undefined behaviour
#1104 opened Aug 14, 2023 by armintoepfer updated Aug 15, 2023
3
ProTip! Exclude everything labeled bug with -label:bug.