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@github-actions github-actions released this 30 Jan 16:55
v0.1.0
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Learn about vigilant mode.

0.1.0 (2026-01-30)

Features

  • add modification rate (#12) (450e586)
  • add option to set lp time limits (#40) (555eef7)
  • add option to set output directory (#44) (0119188)
  • add preprocessing (#21) (40c5214)
  • additionally output sequence with all alternate nucleotides (#42) (675a310)
  • allow both raw and preprocessed data as input (#23) (d4d353a)
  • allow singleton selection for tsv input (#29) (0beb9cd)
  • allow using lp based filter on terminal fragments (#45) (fac53a6)
  • build skeleton and use that to constrain the MILP (15b21bd)
  • enable recomputing of dp table (#22) (5f7ffd7)
  • establish standard unit masses for simplified nucleotide consideration (#15) (ab5206d)
  • estimate sequence length (#20) (a6bc2d6)
  • explain observed masses or mass differences using dynamic programming (#3) (c36b8cc)
  • extend dp to nucleotides (#9) (0b5f411)
  • filter early retention times with noise peaks (#32) (b7b1301)
  • filter fragments with lp (#10) (0b947fc)
  • filter fragments with sequence mass (#16) (d51e573)
  • group same-weight fragments during skeleton building (#17) (e3d34f5)
  • improve sequence length estimation with lp based selection (#26) (b102ffb)
  • plot different fragment classes individually (#46) (281a848)
  • reduce alphabet after skeleton building (#19) (4e95659)
  • set intensity cutoff based on percentile (#41) (cfc1085)

Bug Fixes

  • allow using cli (#13) (09a65af)
  • catch exceptions during lp initialization for ambiguity removal (#39) (4bf108b)
  • catch exceptions if no prediction is possible (#30) (02405e1)
  • catch exceptions while solving lp (#38) (7ea9737)
  • catch nonetype bases during lp evaluation (#37) (4c5c695)
  • ensure correct fragment end indices for lp (#25) (051e744)
  • ensure usage of correct singleton path (#35) (51264eb)
  • filter singletons by combined tag mass (#24) (7b6ab9a)
  • map singletons to mass representative to avoid filtering them out (#33) (82de7e8)
  • plot only one base at each position of global sequence (#34) (f6ec9a2)
  • skip fragments with non-explainable masses during ladder building; allow start fragments to reach the end, and vice versa; non certain start or end fragments may also touch start and end and even span the entire sequence (#7) (9a1f03b)

Performance Improvements

  • further limit MILP by terminal fragment ladder skeleton (6e9b7aa)
Assets 2
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