#320 Large deletions in SAM/BAM glyph display

v2.0
closed-fixed
Lincoln Stein
Gbrowse (196)
5
2010-11-01
2010-07-16
Keiran Raine
No

Hi,

The SAM view of data under gbrowse does not display reads with large deletions correctly. When viewing at base level bgcolor (green) and '-' are seen. Next stage out a thin green line and zoomed out further they become completely undetectable.

I've attached a zip file with an image including the 3 levels of view, along with a BAM file containing the data used to generate the images. Data is mapped against Human GRCh37 (hg19).

Regards,
Keiran

Discussion

  • Keiran Raine
    Keiran Raine
    2010-07-16

    zip containing image and supporting BAM file and index

     
    Attachments
  • Scott Cain
    Scott Cain
    2010-08-03

    • assigned_to: scottcain --> lstein
     
  • Lincoln Stein
    Lincoln Stein
    2010-08-03

    If the deletions are indicated using the CIGAR string, then this is the expected behavior. Additional processing is needed to detect and display large CIGAR deletions, to mirror the way that splices are handled with the "split_splices" option.

     
  • Lincoln Stein
    Lincoln Stein
    2010-11-01

    This is fixed in Bio::Graphics version 2.15

     
  • Lincoln Stein
    Lincoln Stein
    2010-11-01

    • status: open --> closed-fixed