Usage

Supported formats

• BAM (index and sorted). .bai file is needed.
  • Local, AWS, Google Cloud, or HTTP/HTTPS
  • Local: place the .bai file in the same directory; or specify the index file with -i.
  • s3: set credentials in environmental variables. See: https://www.htslib.org/doc/htslib-s3-plugin.html
  • gss: TODO not tested. Please provide feedback if it works!
  • Note that the custom bai path (-i) is not supported for remote use for due to rust-htslib API limitation.

Key bindings

Quit: :q

Normal mode

Command	Notes	Example
:	Enter command mode
h/j/k/l	Move left / down / up / right
y/p	Fast move left / right
w/b	Beginning of the next / previous exon
e/ge	End of the next / previous exon
W/B	Begining of the next / previous gene
E/gE	End of the next / previous gene
z/o	Zoom in / out
{/}	Previous / next chromosome
_number_ + _movement_	Move by _number_ steps	20h: left by 20 bases

Command mode:

Command	Notes	Example
:q	Quit
:h	Help
:_pos_	Go to position on same contig	:1000
:_contig_:_pos_	Go to position on specific contig	:17:7572659
:_gene_	Go to _gene_.	:KRAS
:ls / :contigs	List contigs (j/k to select, Esc, Enter)
Esc	Switch to Normal Mode

Compare TGV and Vim concepts

Command	TGV	Vim	Notes
h/l	Horizontal movement	Character
y/p	Fast horizontal movement	NA	y/p do different things in Vim
w/b/e/ge	Exon	word
W/B/E/gE	Gene	WORD
j/k	Alignment track	Line
z/o	Zoom	NA	o does a different thing in Vim.
{/}	Chromosome	Paragraph