Does IGV support block bgzip compressed and indexed genomes?

[sjackman]

Hi, Jim. Does IGV support block gzip compressed and indexed genomes? For example

bgzip -i genome.fa
samtools faidx genome.fa.gz

Creates the files

• genome.fa.gz Block gzip compressed FASTA file
• genome.fa.gz.gzi Block gzip index file
• genome.fa.gz.fai FASTA index

[jrobinso]

No it doesn't.

On Mon, Oct 3, 2016 at 11:22 AM, Shaun Jackman notifications@github.com
wrote:

Hi, Jim. Does IGV support block gzip compressed and indexed genomes? For
example

bgzip -i genome.fa
samtools faidx genome.fa.gz

Creates the files

• genome.fa.gz: Block gzip compressed FASTA file
• genome.fa.gz.gzi: Block gzip index file
• genome.fa.gz.fai: FASTA index

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
#321, or mute the thread
https://github.com/notifications/unsubscribe-auth/AA49HGFMxOmqgEw67xQNXOzAYGfgPyARks5qwUfkgaJpZM4KM4cQ
.

[sjackman]

Thanks for the quick response, Jim. Feel free to close this issue as answered, or convert it to a feature request if it's a feature that you'd like to support.

[jrobinso]

I'll leave it open, I didn't realize samtools did that.

[jrobinso]

@sjackman I'm trying to add support for this, but I can't find a description anywhere of the ".gzi" file. I've looked in all the usual places. Do you have a description of this file? Its essential, the .fai file is not granular enough.

[sjackman]

I haven't found a spec. I believe bgzf_index_load_hfile is the code to read the .gzi file format:
https://github.com/samtools/htslib/blob/master/bgzf.c#L1760
It looks like the first 8 bytes (uint64_t) are the number of blocks, n, followed by n pairs of uint64_t offsets, the first offset is the offset into the uncompressed file, and the second offset is the corresponding offset into the compressed file.

[sjackman]

Cool! Thanks, Jim! I look forward to testing it out.

[jrobinso]

It helps a lot with cram files, where the entire sequence for a chromosome is needed.