samtools tview -d T problem

[nielsl]

Samtools gurus,

I would like to generate multiple text files with alignment regions
like that shown in the attached tview.png, which is a screenshot
from the interactive tview. When tview is given the -d T option,
the region is truncated (see tview-d.png) and I do not see a mpileup
option for it. It would be good if -p seq:from-to was possible with
tview, but its not. How is this done?

Niels L

[lindenb]

as far as I remember, tview use the env variable ${COLUMNS} . If this variable is not set, 80 is used by default. http://pubs.opengroup.org/onlinepubs...bd/envvar.html

if COLUMNS is not set, try:

export COLUMNS=200

[nielsl]

That worked - merci, bravo. I can now let the script set that variable for each desired region. I will suggest they extend the -p option to accept from:to instead of just from, though.

[nielsl]

ps - well, the number of columns needed to accomodate all sequences so they line up is not known before the tview routine is finished. So really, setting COLUMNS to a fixed value is only half a solution and a tview option is needed. Either that, or an option for mpileup that shows the alignment the same way as tview, instead of rotating it 90 degrees. I will ask them, but the samtools mailing list has not responded to new subscription requests for a few days.

[lindenb]

That worked - merci, bravo. I can now let the script set that variable for each desired region. I will suggest they extend the -p option to accept from:to instead of just from, though.

not so easy as tview displays the insertions in the reads. So if you have a very large insertion the screen matrix could be very large. That is why tview only use a starting position.

FYI , I wrote a small tool displaying the BAM as a SVG file: https://github.com/lindenb/jvarkit/wiki/Bam2SVG

[nielsl]

Ah thanks. Well I resorted to extending the columns, check ends, trim and show. I am using it for a quick one-off thing, but thank you for the link, its useful. I got some old alignment viewer archaeology from 2005 that used Perl PDL, there is still a copy alive here, on a tiny and slow VM: http://rnp.uthscsa.edu:8001/UTHSCSA/...i?menu_1=tmrnp .. it removes gap-only columns at display time, which samtools cannot ( true?). There is also a html tree browser (click Organisms).