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Added support for persisting IndexedReads index to disk #1037

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Added support for persisting IndexedReads index to disk #1037

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10 changes: 9 additions & 1 deletion pysam/libcalignmentfile.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ from pysam.libcutils cimport force_bytes, force_str, charptr_to_str
from pysam.libcutils cimport encode_filename, from_string_and_size
from pysam.libcalignedsegment cimport makeAlignedSegment, makePileupColumn
from pysam.libchtslib cimport HTSFile, hisremote

import json
if PY_MAJOR_VERSION >= 3:
from io import StringIO
else:
Expand Down Expand Up @@ -2918,6 +2918,14 @@ cdef class IndexedReads:
self.htsfile = self.samfile.htsfile
self.header = samfile.header
self.owns_samfile = False

def store(self, filename):
with open(filename, 'w') as f:
json.dump(self.index, f)

def load(self, filename):
with open(filename) as f:
self.index = json.load(f)

def build(self):
'''build the index.'''
Expand Down