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Need to flush the output pretty frequently to keep memory usage down

                        H5.create_dataset(chrom, (chrom_len, 6), compression='gzip', compression_opts=6, chunks=(mi
n(chrom_len,100000),6), fillvalue=-1, dtype='i')
                # Skip the first line
                firstLine = IM.readline()
                #chr     pos     strand  context ratio   eff_CT_count    C_count CT_count        rev_G_count     re
v_GA_count    CI_lower        CI_upper
                #test1   14      -       CHG     0.000   1.00    0       1       0       0       0.000   0.793
                for i,line in enumerate(filter(lambda x: x[0] != "#", IM)):
                        tmp = line.split('\t')
                        chrom, pos, strandIndex = (tmp[0], int(tmp[1])-1, self.strands.index(tmp[2]))
                        cIndex = self.contexts.index(tmp[3])
                        c, ct, g, ga = map(int, tmp[6:10])
                        # Set record
                        H5[chrom][pos] = (cIndex, strandIndex, c, ct, g, ga)
                        if i%100 == 0:                                                                             
                                H5.flush()