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- from frst.dependences import pybam
-
- def parse_bam(bam_file):
- cov = {}
- cov_val = 0
- for alignment in pybam.read(bam_file):
- #pos 1 based (see Pybam doc)
- start_pos = alignment.sam_pos1
- end_pos = alignment.sam_pos1 + alignment.sam_block_size
- if start_pos not in cov:
- cov[start_pos] = 0
- if end_pos not in cov:
- cov[end_pos] = 0
- # add a weight on the start and lower on the end
- cov[start_pos] = cov_val +1
- cov[end_pos] = cov_val -1
- return cov
|
