This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to use samtools tview goto with long reference sequence name

I'm sorry if the answer to this is blatantly obvious...

I'm trying to jump to a sequence region in samtools tview with the (g)oto command. The problem is I can't enter the full command due to size restrictions of the input section.

I want to enter:

Goto: d62ff96e-317e-46d3-92b5-f5a4b329694f:3598

but I can only enter:

Goto: d62ff96e-317e-46d3-92b5-f5a4b329694f:359

Any tips?

samtools tview reference goto
• 3,822 views • link
updated by John Marshall John Marshall • written by quokka • quokka

3 answers

edit the file https://github.com/samtools/samtools/blob/50a0bafe616a822df2f98dc4635840e430cbea45/bam_tview.h

change https://github.com/samtools/samtools/blob/50a0bafe616a822df2f98dc4635840e430cbea45/bam_tview.h#L80

#define TV_MAX_GOTO 40

to a larger value like

#define TV_MAX_GOTO 50

and recompile samtools

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Ah. Excellent. Not so obvious then. Thanks!

• 1 views • link
written by quokka • quokka

Hi, If this was the answer to your question please accept it as a right answer.

enter image description here

• 1 views • link
written by Medhat Medhat

A shameless plug... If you use samtools tview you may be interested in ASCIIGenome

• 1 views • link
written by dariober dariober

Sadly this text entry box is too narrow for unfortunate contigs named via UUIDs. See PR samtools/samtools#968.

In the meantime, there is a workaround to jump to the position you're after using a vanilla samtools tview build: the goto command accepts =1234 to jump to a position on the current chromosome. So you can jump to where you want in two hops:

  1. Goto d62ff96e-317e-46d3-92b5-f5a4b329694f which takes you to the start of that contig;
  2. Goto =3598 to jump to the desired position.
• 1 views • link
written by John Marshall John Marshall

Log in to answer this question.

More posts like this