# Path: seqio.py
# def fastaIterator(fh):
# 
#     l = fh.readline()
#     if(not l or not l.startswith(">")):
#         raise Exception("No \">\" at start of Fasta File")
#     name = l.strip()[1:]
#     seq = ""
#     while True:
#         l = fh.readline()
#         if not l or l.startswith(">"):
#             yield FastaRecord(name,seq)
#             if not l:
#                 break
#             name = l.strip()[1:]
#             seq = ""
#         else:
#             seq += l.strip()
# 
# Path: cov.py
# def getMarkedRanges(v):
#     '''Takes an array v with wanted elements marked as 1
#     all other elements are 0. This function returns
#     the index ranges of these 1's'''
#     
#     #subtract adjacent elements to find -1
#     #flip these to 1's and change everything else to 0
#     #so that we can use it to find the index
#     breaks = map(lambda x: 1 if x == -1 else 0 , pairwise(v + [0],operator.sub))
# 
#     #create a cumsum of the inverse to know how many elements
#     #are a part of this region
#     lengths = accumulate_mod(v)
# 
#     #zip up the indexes with the lengths
#     z = zip(count(),list(lengths))
# 
#     #use the breaks to select only the indexes we want
#     #and use the cumsum to know how many elements came
#     #previously
#     endAndLength = compress(z,breaks)
# 
#     return map(lambda (e,l): (e-l+1,e), endAndLength)
# 
# Path: misc.py
# def create_enum(**enums):
#     return type('Enum', (), enums)


import sys
import copy
from nucio import *
from seqio import fastaIterator
from operator import itemgetter
from itertools import groupby, repeat, izip_longest, imap, count, chain
from collections import namedtuple
from cov import getMarkedRanges
from misc import create_enum
#!/usr/bin/env python






if not len(sys.argv) == 7:
    print "pb_correct.py in.fa in.snps in.showcoords clr_id(float) min_read_length out_prefix"
    sys.exit(1)

CLR_ID_CUTOFF = float(sys.argv[4])
MIN_READ_LENGTH = int(sys.argv[5])

PileupEntry = namedtuple("PileupEntry", ["index","base","snps","utg","clr"])
CovStat = {"COVERED":"COVERED", "UNCOVERED":"UNCOVERED", "JOINED":"JOINED"}

class CoverageRange:
    def __init__(self, b, e, pid, covstat):
        self.begin = b
        self.end = e
        self.pctid = pid
        self.covstat = covstat


# Path: seqio.py
# def fastaIterator(fh):
# 
#     l = fh.readline()
#     if(not l or not l.startswith(">")):
#         raise Exception("No \">\" at start of Fasta File")
#     name = l.strip()[1:]
#     seq = ""
#     while True:
#         l = fh.readline()
#         if not l or l.startswith(">"):
#             yield FastaRecord(name,seq)
#             if not l:
#                 break
#             name = l.strip()[1:]
#             seq = ""
#         else:
#             seq += l.strip()
# 
# Path: cov.py
# def getMarkedRanges(v):
#     '''Takes an array v with wanted elements marked as 1
#     all other elements are 0. This function returns
#     the index ranges of these 1's'''
#     
#     #subtract adjacent elements to find -1
#     #flip these to 1's and change everything else to 0
#     #so that we can use it to find the index
#     breaks = map(lambda x: 1 if x == -1 else 0 , pairwise(v + [0],operator.sub))
# 
#     #create a cumsum of the inverse to know how many elements
#     #are a part of this region
#     lengths = accumulate_mod(v)
# 
#     #zip up the indexes with the lengths
#     z = zip(count(),list(lengths))
# 
#     #use the breaks to select only the indexes we want
#     #and use the cumsum to know how many elements came
#     #previously
#     endAndLength = compress(z,breaks)
# 
#     return map(lambda (e,l): (e-l+1,e), endAndLength)
# 
# Path: misc.py
# def create_enum(**enums):
#     return type('Enum', (), enums)


# Path: pb_correct.py
import sys
import copy
from nucio import *
from seqio import fastaIterator
from operator import itemgetter
from itertools import groupby, repeat, izip_longest, imap, count, chain
from collections import namedtuple
from cov import getMarkedRanges
from misc import create_enum

#!/usr/bin/env python






if not len(sys.argv) == 7:
    print "pb_correct.py in.fa in.snps in.showcoords clr_id(float) min_read_length out_prefix"
    sys.exit(1)

CLR_ID_CUTOFF = float(sys.argv[4])
MIN_READ_LENGTH = int(sys.argv[5])

PileupEntry = namedtuple("PileupEntry", ["index","base","snps","utg","clr"])
CovStat = {"COVERED":"COVERED", "UNCOVERED":"UNCOVERED", "JOINED":"JOINED"}

class CoverageRange:
    def __init__(self, b, e, pid, covstat):
        self.begin = b
        self.end = e
        self.pctid = pid
        self.covstat = covstat


    def __repr__(self):