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liyan910117

pairedbamtobed12's Issues

Add support for non-proper pairs.

If read 2 is unmapped or not properly aligned, it should be (optionally ?) possible to represent read 1 as a BED12 line. The problem with read 2 could be reported as a different colour code or score, for instance. Doing the converse with read 2 may not be a good idea, unless it is strictly opt-in, since we use the BED12 format to derive 5′ ends, and that information is carried by read 1 in our data.

Breaks if Read1 and Read2 overlap on a splice junctions.

With reads that are long enough to overlap over a splice junction, the computation of the BED12 blocs will bug and produce improper lines.

For example:

V300073286L2C005R0180080888;RQ:0.00	99	chr1	579808	60	1S122M43N26M	=	579866	149	GAGAAGGAGAGAAAAAATAAAGATAAAAATAATGAAGCTTCTCTTTTTGTTTGTCGGGCTGAGCATGGCCGGAACAAAATGCTCCGGGGACATGTGCTGGGCTCAAGAGATGAGAGGACCAAGACCCCGACGAACTGAGAAAAGCGACG	'FFDEF0CGDFFG@@?DFFFF@?>G?GFGGFFBFDCEBC?EFFEG=BGEFGBFGG@0GFFB33FGBFEAG;F;B4DGEDD:GCGED<FG=FA@GEG3EGBFGGGEFE9;GED?FGCD>EEE5B<FAECDFGF:FE@EB9GFDC@BFBG2	AS:i:-21	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:15G25T8C35A61	YS:i:-10	YT:Z:CP	RG:Z:DE1_T1_no	XS:A:+	NH:i:1
V300073286L2C005R0180080888;RQ:-1.00	147	chr1	579866	60	64M43N52M	=	579808	-149	TGAGCATGGCGGGACCAAAATGCTCCGGGGACATGTGCTGGGCTCAAGAGATGAGAGGACCAAGACCCCGACGAACTGAGAAAAGCGACGAATGCTCAATTGATGCGCACAAAACC	@G<1DE9D98&CD@4(GFA6:F68B6DCGG.?F>FFFG<BCD2&5DEGFFCCFGG?G?;DFFCG6G0FBFF/F?FF>FFGDEEAEEFDCF>FFD>-FFBFFGFEDFE:AF>GBBBB	AS:i:-10	ZS:i:-20	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:10C3A13A87	YS:i:-21	YT:Z:CP	RG:Z:DE1_T1_no	XS:A:+	NH:i:1

Will give:

 chr1	579807	580024	V300073286L2C005R0180080888;RQ:0.00	120	+	579807	579998	255,0,0	4	122,26,64,52	0,165,58,165

(note that 58 < 165)

Color the reads according to strand.

Currently, all reads are colored to red (255,0,0). It would be good to color them according to strand, like in the zenbu browser.

In the meantime, the following one-linder will do.

awk '{OFS="\t"}{if($6=="+"){$9="0,120,0"};if($6=="-"){$9="128,0,128"};print}'

Add an ATAC-seq mode

This mode will:

  • Add 4 to start positions and subtract 5 to the end positions, so that neighbour tagments do not overlap,
  • have a single bloc, since there is no splicing, and
  • indicate the centre of the interval as a thick region.

Please do not hesitate to submit a pull request if you are faster than me. I can not start to work on this until October.

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