yiq / bamstatsalive Goto Github PK

Generate read depth histogram, in which

X-axis: read depth (1x, 2x, ...)
Y-axis: number of positions

Implement the feature that keeps track of the changes in the statistics, and terminate the calculation when the statistics stabilizes. Method of calculating changes need to be developed.

Allow the ability to look at base quality from each sequencing cycle if read group info is in the header.

In order to correctly process an entire BAM file, which could potentially contains more than one chromosome, special cares need to be given at the chromosome boundaries. The code need to be audited so that such boundaries will not cause undesirable effects on the statistics.