BamSlider

An experimental sliding window for BAM/SAM files using Python's deques. This is all in alpha, but I hope to develop it as I get more time.

BamSlider is a iterator class. You can use it like so:

slider = BamSlider("test.sorted.sam", size=10000, step=5000)
for window, reads in slider:
    print window, [r.mapq for r in reads]

Each window here is a named tuple of seqname (i.e. chromosome or contig name), start position, and end position. reads is a list of all reads with start positions in this window. Note that pairing is not explicitly handled.

Todo

• Unit testing -- high priorty
• Maybe add option to handle pairing of properly-paired reads. This would require using a dictionary to group reads, for efficiency.