LICENSE
MANIFEST.in
README.md
pyproject.toml
phased_methylation.egg-info/PKG-INFO
phased_methylation.egg-info/SOURCES.txt
phased_methylation.egg-info/dependency_links.txt
phased_methylation.egg-info/entry_points.txt
phased_methylation.egg-info/requires.txt
phased_methylation.egg-info/top_level.txt
src/phased_methylation/__init__.py
src/phased_methylation/call.py
src/phased_methylation/check_gpu_availability.py
src/phased_methylation/env.py
src/phased_methylation/export_bedgraph.py
src/phased_methylation/export_metilene.py
src/phased_methylation/gene_body_methylation.py
src/phased_methylation/intersect.py
src/phased_methylation/map.py
src/phased_methylation/mean.py
src/phased_methylation/merge.py
src/phased_methylation/methylation_kde.py
src/phased_methylation/parse_gff.py
src/phased_methylation/phase.py
src/phased_methylation/phased_methylation.py
src/phased_methylation/plot.py
src/phased_methylation/plot_bedtools.py
src/phased_methylation/plot_genes.py
src/phased_methylation/plot_repeats.py
src/phased_methylation/promoter_methylation.py
src/phased_methylation/run.py
src/phased_methylation/split_methyl_bed.py
src/phased_methylation/tabulate.py
src/phased_methylation/ecoli_example_data/draft.fa
src/phased_methylation/ecoli_example_data/reads.fasta
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch107_read4268_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch109_read2202_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch111_read2109_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch111_read5041_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch118_read886_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch123_read2477_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch123_read955_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch139_read6216_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch144_read1044_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch158_read5484_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch170_read4483_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch174_read3654_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch177_read1452_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch179_read1009_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch196_read2318_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch200_read6055_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch21_read1037_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch24_read2302_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch250_read878_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch280_read2154_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch280_read913_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch281_read4019_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch289_read1687_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch289_read2189_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch28_read503_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch290_read1002_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch290_read2497_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch292_read1173_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch294_read1069_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch302_read1093_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch302_read6122_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch309_read4050_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch316_read4806_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch316_read5270_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch326_read4256_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch342_read2347_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch350_read270_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch353_read1369_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch355_read2033_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch361_read1047_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch361_read4057_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch378_read4280_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch378_read4310_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch378_read4497_strand1.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch378_read5665_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch378_read929_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch381_read3165_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch383_read6112_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch391_read2287_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch391_read3493_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch403_read4689_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch407_read2873_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch40_read4532_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch418_read2596_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch41_read2892_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch420_read357_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch427_read1086_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch432_read393_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch433_read1144_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch43_read1483_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch43_read1894_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch43_read2386_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch43_read3275_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch43_read394_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch442_read1231_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch442_read5435_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch44_read3066_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch460_read2786_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch460_read2860_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch467_read81_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch471_read263_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch477_read112_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch47_read328_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch47_read924_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch481_read1028_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch481_read1935_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch481_read715_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch482_read758_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch483_read1308_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch483_read811_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch485_read77_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch486_read3631_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch490_read814_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch491_read3080_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch493_read2488_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch493_read5399_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch497_read3630_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch501_read29_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch505_read1993_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch505_read3234_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch506_read899_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch54_read3215_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch54_read3907_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch57_read1147_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch57_read3088_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch57_read3412_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch64_read1905_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch64_read6087_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch66_read4851_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch69_read998_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch7_read2760_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch80_read1993_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch84_read4752_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch84_read564_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch85_read2098_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch85_read498_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch8_read1768_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch91_read2127_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch95_read114_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch95_read4662_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch98_read2298_strand.fast5
src/phased_methylation/ecoli_example_data/fast5_files/odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch98_read2551_strand.fast5
src/phased_methylation/longshot_example_data/genome.fa
src/phased_methylation/longshot_example_data/genome.fa.fai
src/phased_methylation/longshot_example_data/ground_truth_variants.vcf.gz
src/phased_methylation/longshot_example_data/ground_truth_variants.vcf.gz.tbi
src/phased_methylation/longshot_example_data/out.vcf.gz
src/phased_methylation/longshot_example_data/out.vcf.gz.tbi
src/phased_methylation/longshot_example_data/pacbio_reads_30x.bam
src/phased_methylation/longshot_example_data/pacbio_reads_30x.bam.bai
src/phased_methylation/minimap2_example_data/MT-human.fa
src/phased_methylation/minimap2_example_data/MT-orang.fa
src/phased_methylation/minimap2_example_data/test.bam
src/phased_methylation/minimap2_example_data/test.bam.bai
test/test_ecoli.py
test/test_longshot.py
test/test_minimap2.py