[Gmod-ajax] Alignments2: Callback for read colouring

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[Gmod-ajax] Alignments2: Callback for read colouring

Keiran Raine
Hi,

I want to add a callback for the colouring of reads in our view but I need to know what the names for several of the SAM/BAM fields would be when addressing them from JS.

What we want to achieve is the following panel of colour variation (colours not set in stone)

Properly paired (as defined by aligner) Forward/Reverse:
Red/Blue (as currently)
Different Chromosome:
Orange/Green
Both same orientation (FF/RR):
Yellow/Violet
Mate unmapped
Hard red/Hard blue
Other:
black

To be able to do this I need to be able to access the following SAM/BAM fields

FLAG,RNAME,POS,RNEXT,PNEXT

(or expanded set bits of flag).

If someone could point me him the correct direction I'd really appreciate it.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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