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Alignments2 mate highlight fix #986

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merged 7 commits into from Feb 28, 2018

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rdhayes commented Feb 13, 2018

Fixes #907

I opted for two changes to BAM/LazyParser.js, with associated updates to highlight attributes in Alignments2 menuTemplate:

  1. New next_segment_position_highlight() to return the non-intuitive Location format to cause a single line highlight at the starting base (e.g. Chr01:20..19 will draw a line between bases 19 and 20). Start from feature.get('_next_pos') is incremented from BAM 0-based coordinate to highlight at the correct base.

  2. The existing next_segment_position() function is now only used in Alignments2 menuTemplate title attributes, where again incrementing feature.get('_next_pos') by 1 to get the correct display coordinates in 1-space seems correct.

rdhayes added some commits Feb 13, 2018

add new function next_segment_position_highlight to return a location…
… string in the format ref:N..N-1 to place a line highlight interbase between N-1 and N; update to add 1 to feature.get('_next_pos') in function next_segment_position, to return single-base ref:N coordinates as 1-based (next_segment_position now only used in menu item titles)
update mate pair menu items to configure a highlight at the new next_…
…segment_position_highlight location string (ref:N..N-1 to add a line highlight just before base N)

@wafflebot wafflebot bot added the in progress label Feb 13, 2018

rdhayes and others added some commits Feb 13, 2018

@rbuels rbuels added this to the 1.12.5 milestone Feb 27, 2018

@rbuels rbuels merged commit dd9cbc6 into dev Feb 28, 2018

@wafflebot wafflebot bot removed the in progress label Feb 28, 2018

@rbuels rbuels deleted the Alignments2_mateHighlightFix branch Feb 28, 2018

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