from libc.stdint cimport uint32_t, uint8_t, uint64_t, int64_t
from libc.math cimport sqrt
from cpython cimport PyBytes_FromStringAndSize
from pysam.chtslib cimport bam1_t, bam_pileup1_t
from pysam.cfaidx cimport FastaFile
from pysam.calignmentfile cimport AlignmentFile, IteratorRowRegion
from pysam.calignedsegment cimport pysam_bam_get_cigar, pysam_bam_get_seq, \
    pysam_bam_get_qual, PileupColumn
