Java Library For Reading Bai Files And Understanding Index With Respect To Bam

Question

[User 9906]

Hi,

1. Is there a library in java which allows me to read BAM index files(.bai) ?

2. I want to understand how the index maps to BAM files' particular location. How do I get to directly reach a particular file location to read instead of parsing from the start of the file. Please suggest a good read for this.

3. Is it possible to deduce a particular byte to read in the BAM file by reading the index in the BAI ?

Thank You for your help.

Answer 1

[Gww]

The picard library implements samtools in java. For more specific information about how BAM files are indexed check out the samtools format specification.

Answer 2

[Pierre Lindenbaum]

Don't reinvent the wheel an use the picard API. see this post for a simple code. You can get an iterator for a given genomic segment using http://picard.sourceforge.net/javadoc/net/sf/samtools/SAMFileReader.html#queryOverlapping%28java.lang.String,%20int,%20int%29

the SAM specs describes the bai indexes as a bin index ( see this post)