Issues

• hisat2_extract_snps_haplotypes_VCF.py: IndexError on haploid genotypes silently truncates chrX to PAR1

  DaehwanKimLab/hisat2#475 · Filter by author iandriver opened on Aug 29, 2026

• hisat2-build: .7 index file is not byte-reproducible across C++ standard libraries (unstable sort on _haplotypes)

  DaehwanKimLab/hisat2#474 · Filter by author iandriver opened on Aug 23, 2026

• hisat2-build silently drops a large fraction of variants from the local indexes, and hisat2-inspect still reports all of them

  DaehwanKimLab/hisat2#473 · Filter by author iandriver opened on Aug 13, 2026
  2

• A SNP-aware index never reports the spliced alignment when an equal-scoring contiguous match exists elsewhere

  DaehwanKimLab/hisat2#472 · Filter by author iandriver opened on Aug 9, 2026

• local_max_gbwt leads to blowup on moderate size human chr1 vcf-derived snp/haplotypes

  DaehwanKimLab/hisat2#470 · Filter by author mkarikom opened on Jul 9, 2026
  1

• hisat2-build segmentation fault

  DaehwanKimLab/hisat2#468 · Filter by author estolle opened on Jun 9, 2026
  1

• Segmentation fault

  DaehwanKimLab/hisat2#467 · Filter by author Helyem opened on Apr 6, 2026

• HISAT-3N: silently ignores read pairs when --repeat is set

  DaehwanKimLab/hisat2#465 · Filter by author ankebusch opened on Dec 10, 2025

• Default format parsing in HISAT2 causes incorrect read length calculation.

  DaehwanKimLab/hisat2#464 · Filter by author huangl-CAU opened on Nov 13, 2025

• Hisat3n-table: unexpected strand info and missing sites?

  DaehwanKimLab/hisat2#461 · Filter by author ZqF2017 opened on Sep 26, 2025

• long time no result , and big running memory usage?

  DaehwanKimLab/hisat2#460 · Filter by author nianxt opened on Aug 7, 2025
  1

• HISAT2 missed reads which can be aligned to genome

  DaehwanKimLab/hisat2#459 · Filter by author santataRU opened on Jul 9, 2025

• max-intronlen controls "concordant pair" alignment flags - that should not be the case

  DaehwanKimLab/hisat2#458 · Filter by author therealgenna opened on Jul 8, 2025

• error running hisat2-align-s Error reading _rstarts[] array: 7876, 7896

  DaehwanKimLab/hisat2#457 · Filter by author jazberna1 opened on Jul 2, 2025

• Error during index built

  DaehwanKimLab/hisat2#456 · Filter by author desmodus1984 opened on Jun 26, 2025

• memory usage hisat2-align died with signal 9 (KILL)

  DaehwanKimLab/hisat2#455 · Filter by author murheisa opened on Jun 14, 2025
  2

• Errors when chromosome length is >2G

  DaehwanKimLab/hisat2#454 · Filter by author xiekunwhy opened on Jun 4, 2025
  1

• Long time no results！

  DaehwanKimLab/hisat2#453 · Filter by author zhangwenda0518 opened on May 14, 2025
  2

• Piping reads from stdin fails for hisat2 alignment

  DaehwanKimLab/hisat2#451 · Filter by author sterrettJD opened on Apr 18, 2025
  2

• very large memory usage

  DaehwanKimLab/hisat2#450 · Filter by author diekhans opened on Apr 3, 2025
  8

• un-conc output fail

  DaehwanKimLab/hisat2#449 · Filter by author RafaellaFerraz opened on Mar 17, 2025

• hisat-3n-table

  DaehwanKimLab/hisat2#448 · Filter by author wingrew opened on Jan 20, 2025

• (ERR): Expected hisat2 to be in same directory with hisat2-align-s and hisat2-align-l:

  DaehwanKimLab/hisat2#446 · Filter by author mcastilloli2 opened on Dec 11, 2024
  1

• --sra-acc argument behavior

  DaehwanKimLab/hisat2#444 · Filter by author el239 opened on Nov 13, 2024

• Should I run hisat2 in a 2-pass mode for better mapping at novel junctions?

  DaehwanKimLab/hisat2#443 · Filter by author weishwu opened on Nov 9, 2024