purpose of faidx and bai

[bioxyz]

Hello,
What is the purpose of faidx and bai?

Is it possible to view faidx and bai?

Are they any examples how is it possible to use faidx and bai in a programming language?

Thank you in advance.

[Thomas Doktor]

As far as I know, the purpose of the index files are to allow fast and memory-efficient retrieval of alignments/subsequences in specific regions. They contain non-human readable binary content and are really only useful in combination with the BAM or FASTA file they were made for.

[bioxyz]

Sounds good.

Are there any examples how to use fast and memory-efficient retrieval of informations?

[Thomas Doktor]

I would look at the source code for various open source genome browsers, like Gambit which is from the Marth lab.

[nilshomer]

Hello,
What is the purpose of faidx and bai?

Is it possible to view faidx and bai?

Are they any examples how is it possible to use faidx and bai in a programming language?

Thank you in advance.

The faidx is the index file for a reference sequence (FASTA format), while the bai is an index file for the read alignments (SAM format). They can be generated using SAMtools or Picard, with both having a C and Java API, respectively, to give you access to these files.

[bioxyz]

Do you know about any examples how to use faidx and bai with C or Java API or any technical explanation how the both files are working?

[nilshomer]

Do you know about any examples how to use faidx and bai with C or Java API or any technical explanation how the both files are working?

Here's the Picard API documentation.

Here's the Samtools API documentation.

The rest can be found in the two source codes (the best documentation of them all).