Opened 8 years ago

Closed 8 years ago

Last modified 13 months ago

#631 closed defect (fixed)

arb_pars does no longer reject sequences with insufficient data

Reported by: westram Owned by: westram
Priority: major Milestone: arb7.0
Component: ARB_PARSIMONY Version: SVN
Keywords: Cc:

Description (last modified by westram)

  • database: prot_pars_test.arb
  • detailed description of problem see msgid 54882B19.5060500@…

Change History (8)

comment:1 Changed 8 years ago by westram

  • Status changed from new to assigned

comment:2 Changed 8 years ago by westram

  • Status changed from assigned to _started

comment:3 follow-up: Changed 8 years ago by westram

  • Description modified (diff)
  • most likely broken by [878]
  • detection of "too short" sequences was not working for protein alignments
    • fixed by [13453]
    • quick-add now crashes (while destroying short sequences)
      #0  TreeNode::destroy (this=0xcbed40) at /home/ralf/ARB-bilbo/ARB.pars.refactor/INCLUDE/TreeNode.h:258
      #1  0x00000000004d70db in TreeNode::destroy (that=0xcbed40) at /home/ralf/ARB-bilbo/ARB.pars.refactor/INCLUDE/TreeNode.h:280
      #2  0x00000000004d70f5 in destroy (that=0xcbed40) at /home/ralf/ARB-bilbo/ARB.pars.refactor/INCLUDE/TreeNode.h:381
      #3  0x00000000004aa76b in insert_species_in_tree (key=0xcbebc0 "EnbC1314", leaf=0xcbed40, isits=0x7fffffffd300) at PARS_main.cxx:220
      #4  0x00000000004ab445 in hash_insert_species_in_tree (key=0xcbebc0 "EnbC1314", leaf=13364544, cd_isits=0x7fffffffd300) at PARS_main.cxx:347
      #5  0x00007ffff7a3c8b1 in GBS_hash_do_sorted_loop (hs=0xcbe700, func=0x4ab412 <hash_insert_species_in_tree(char const*, long, void*)>, sorter=0x4aa4e8 <sort_sequences_by_length(char const*, long, char const*, long)>, client_data=0x7fffffffd300) at adhash.cxx:658
      #6  0x00000000004ab7c8 in nt_add (agt=0xbd9580, what=NT_ADD_MARKED, quick=true) at PARS_main.cxx:428
      #7  0x00000000004ac9a9 in nt_add_and_update (ntw=0xbd9800, what=NT_ADD_MARKED, quick=true) at PARS_main.cxx:868
      #8  0x00000000004aca10 in NT_add_quick (ntw=0xbd9800, what=NT_ADD_MARKED) at PARS_main.cxx:873
      #9  0x00000000004ae1cb in pars_start_cb (aw_parent=0x851890, wfilt=0x868b10, cmds=0x7fffffffe160) at PARS_main.cxx:1206
      
      Also test for RNA/DNA!

comment:4 in reply to: ↑ 3 ; follow-up: Changed 8 years ago by westram

  • quick-add now crashes (while destroying short sequences) Also test for RNA/DNA!

crashes for RNA/DNA as well

comment:5 in reply to: ↑ 4 Changed 8 years ago by westram

  • Resolution set to fixed
  • Status changed from _started to closed
  • quick-add now crashes (while destroying short sequences) Also test for RNA/DNA!

crashes for RNA/DNA as well

fixed by [13454]

comment:6 Changed 8 years ago by westram

[13457] adds a general test against low amount of sequence data (< 20bp) or too restrictive filtering

comment:7 Changed 7 years ago by westram

  • Milestone set to arb6.1

mark changes that got fixed after arb 6.0.x

comment:8 Changed 13 months ago by westram

  • Milestone changed from arb6.1 to arb7.0

Milestone renamed

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