Opened 5 years ago

Closed 5 years ago

#504 closed misbehavior (fixed)

external aligners complain about changed sequence checksums

Reported by: westram Owned by: westram
Priority: normal Milestone: arb6.1
Component: External_tools Version: SVN
Keywords: Cc:

Description (last modified by westram)

Reproduce:

⇒ warns about sequence checksum change

Warning is caused by aligner changing all 'U' into 'T'

  • in case of RNA alignment, revert that change before calculating checksum by [12821]
    • currently done for any alignment
    • [12829] always converts 'T' or 'U' as expected by alignment type, but
      • again reports wanted checksum failures
      • does not convert when aligner input/output are equal, but wrong "T or U" is used throughout one sequence by [12830]
  • be more severe on that warning, making clear that the sequence data was modified, not some gaps or sth by [12821]

Related TODOs:

  • do not ask whether to overwrite species or sequence when GDE_export is called after aligning by [12818]
  • do not wait for key-press if no error?
  • auto-format affected alignment by [12813]

Change History (9)

comment:1 Changed 5 years ago by westram

  • Description modified (diff)
  • Summary changed from clustalW complains about changed sequence checksums to external aligners complain about changed sequence checksums

comment:2 Changed 5 years ago by westram

  • Description modified (diff)

comment:3 Changed 5 years ago by westram

  • Owner changed from devel to westram
  • Status changed from new to _started

comment:4 Changed 5 years ago by westram

  • Description modified (diff)

comment:5 Changed 5 years ago by westram

  • Description modified (diff)

comment:6 Changed 5 years ago by westram

  • Description modified (diff)

comment:7 Changed 5 years ago by westram

  • Description modified (diff)

comment:8 Changed 5 years ago by westram

  • Description modified (diff)

comment:9 in reply to: ↑ description Changed 5 years ago by westram

  • Resolution set to fixed
  • Status changed from _started to closed

by [12834]

  • do not wait for key-press if no error?

will be (implicitly) implemented by #595

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