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.
- 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.