Issues

• Wrong mutation ages after running merge_ARG.py

  popgenmethods/SINGER#50 · Filter by author pierrefaux opened on Jul 9, 2026
  1

  

• VCF parser treats non-"1" coding as "0"

  popgenmethods/SINGER#46 · Filter by author nspope opened on May 25, 2026

• Possible typo in singer_master in v0.1.9

  popgenmethods/SINGER#43 · Filter by author Jesson-mark opened on Apr 21, 2026

• compute_trace.py confuses -prefix and Ne?

  popgenmethods/SINGER#42 · Filter by author ShuzheGuan opened on Apr 2, 2026
  1

• Different allele counts for vcf and tree file.

  popgenmethods/SINGER#41 · Filter by author jodyhey opened on Feb 3, 2026

• Incomplete parallel run due to "auto-debug" failed

  popgenmethods/SINGER#40 · Filter by author rpianezza opened on Feb 3, 2026
  3

• issues converting parallel_singer output to tskit trees

  popgenmethods/SINGER#39 · Filter by author h-pawar opened on Jan 20, 2026
  5

• Unexpected trend in diversity_fit_mse convergence plot

  popgenmethods/SINGER#38 · Filter by author zhangming-m opened on Jan 4, 2026
  3

• SINGER isn't coping with .vcf.gz file

  popgenmethods/SINGER#34 · Filter by author moshejasper opened on May 14, 2025
  1

• What about the ancestral stat?

  popgenmethods/SINGER#33 · Filter by author jiangzy26 opened on Apr 19, 2025
  1

• No output from compute_trace.py

  popgenmethods/SINGER#31 · Filter by author EEPuckett opened on Feb 7, 2025
  2

• Differentiating between mono-allelic sites vs missing sites

  popgenmethods/SINGER#29 · Filter by author skhalid7 opened on Jan 9, 2025
  1

• AssertionError: assert t >= min_time

  popgenmethods/SINGER#27 · Filter by author hanyou271 opened on Nov 12, 2024
  2

• Converting to tskit format: file not found

  popgenmethods/SINGER#26 · Filter by author LuisGFdez opened on Nov 8, 2024
  2

• High r/m error, branch assertion failed

  popgenmethods/SINGER#25 · Filter by author Uthara28 opened on Oct 25, 2024

• Cannot find compute_pairwise_coalescence_times.py

  popgenmethods/SINGER#22 · Filter by author Luker121 opened on Sep 15, 2024
  4

• Understanding parallel singer errror

  popgenmethods/SINGER#21 · Filter by author mehakmadhura opened on Jul 18, 2024
  6

• Correspondence between nodes and individuals

  popgenmethods/SINGER#16 · Filter by author TymekPieszko opened on May 30, 2024
  3

  

• Assertion `ws > 0' failed.

  popgenmethods/SINGER#15 · Filter by author baozg opened on May 24, 2024
  13

  

• -resume flag fails because ARG.bin_size is never set

  popgenmethods/SINGER#13 · Filter by author nspope opened on Apr 12, 2024
  9

  

• Auto-debug issues occurred with the custom VCF input file

  popgenmethods/SINGER#12 · Filter by author kirifuji-nagisa opened on Apr 12, 2024

• Set tables.mutations.parent column when converting to tskit

  popgenmethods/SINGER#11 · Filter by author nspope opened on Apr 11, 2024
  4

  

• Returning a "full ARG"

  popgenmethods/SINGER#10 · Filter by author kitchensjn opened on Apr 3, 2024
  13

  

• Auto-restart makes it less obvious when parallel jobs are failing

  popgenmethods/SINGER#9 · Filter by author nspope opened on Apr 3, 2024
  10

  

• releases + static binaries on GitHub

  popgenmethods/SINGER#3 · Filter by author grenaud opened on Mar 18, 2024
  1