[UGENE-5863] Wrong identity filtering in Sanger Created: 03/Nov/17  Updated: 22/Feb/18  Resolved: 23/Nov/17

Status: Closed
Project: UGENE
Component/s: Basic-MSA, Basic-Nucl
Affects Version/s: 1.28
Fix Version/s: 1.28.1

Type: Bug Priority: Blocker
Reporter: Eugenia Pushkova [X] (Inactive) Assignee: Eugenia Pushkova [X] (Inactive)
Resolution: Fixed  
Labels: request, sanger
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Issue Links:
Relates
relates to UGENE-5868 Add the "Read name in result alignmen... Closed
relates to UGENE-5877 Replace the "Identity" value of the "... Closed
relates to UGENE-5870 Specify the identity in the Sanger ma... Closed
Story Points: 1
Assigned Tester: Aleksey Tiunov [X] (Inactive)
Tests Type: GUI automatic
Epic Link: Sanger2
Sprint: DEV-29-1, DEV-29-2
Affect Type: Userdefined

 Description   

The Sanger reads mapping algorithm in UGENE has two steps:

  1. Finding of results with BLAST.
  2. Adjustment of the result with the Smith-Waterman algorithm.

In version 1.28 the value of the "Mapping min identity" parameter in the "Map Sanger Reads to Reference" dialog applies to the first step of the algorithm only. The identity should be checked after the two steps instead.

Note also, that the parameter shouldn't be misinterpreted with the "Identity" value of a BLAST result. The latter one is the identity between the found part of a read with the reference. The "Mapping min identity" parameter specifies required identity between the whole read and the reference.

 Comments   
Comment by Olga Golosova [ 14/Nov/17 ]

Note that the "Mapping min identity" will be renamed to "Mapping min similarity" in UGENE-5868, as besides substitutions the Sanger reads mapping algorithm also takes into account insertions and deletions.

See also this description of the identity and similarity terms.

Comment by Olga Golosova [ 14/Nov/17 ]

I've updated the description of the mapping task and the dialog in on the "Mapping Reads to Reference" documentation page. During the review please update the dialog screenshot and add a screenshot of the report.

Comment by Eugenia Pushkova [X] (Inactive) [ 23/Nov/17 ]

GUI test is GUITest_common_scenarios_sanger::test_0007

Comment by Yuliya Algaer [ 22/Feb/18 ]

Reviewed.

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