Bam dialog matches

[cmdcolin]

This is a PR to address the feature request in #496

The algorithm is able to reconstruct the alignment from the BAM read sequence+MD tag+CIGAR string

I created some test cases to handle some common scenarios addressed by the algorithm (insertion, deletion, soft clipping reads)

[cmdcolin]

we can compare the output of sam2pairwise as a reference for this too. https://github.com/mlafave/sam2pairwise

it seems to match the output as expected

[keiranmraine]

@cmdcolin , the only other thing I'd like to see is (if possible) wrapping the display like GBrowse does, e.g.

[cmdcolin]

@keiranmraine Added that "newline based" rendering behind a config flag (renderAlignment.newlines). Width can be configured as renderAlignment.width

[keiranmraine]

@cmdcolin, that works well thanks!

[keiranmraine]

Any ETA on a merge for this?

[cmdcolin]

I made this feature optional and off by default (i.e. introduce the feature behind a feature flag) so would maybe be safe to merge and interested users can enable it if interested.

[cmdcolin]

Given that this is behind a feature flag, would it be ok to merge this one?

I just know it was requested by @keiranmraine and having something like this available can be pretty useful when inspecting alignments

[cmdcolin]

some screenshots:

normal short read

long read

rna-seq read

note that the alignment is constructed entirely from the MD tag and CIGAR string so it doesn't need to retreive reference sequence track data

[cmdcolin]

I think we're gonna try and get this merged behind feature flag! that way it can get tested and improved :)