setup_birdsuite.py
setup_birdsuite_internal_tools.py
setup_pipeline.py
config/pypirc
config/birdsuite/Install.cfg
config/plinkpipeline/Install.cfg
src/analysis/__init__.py
src/analysis/calc_callrate_stats.py
src/analysis/cnvqc/__init__.py
src/analysis/cnvqc/collapse_cnvs.py
src/analysis/tagging/__init__.py
src/analysis/tagging/tagRegions.py
src/birdsuite/__init__.py
src/birdsuite/birdseed_qc_report.py
src/birdsuite/birdseedqc.py
src/birdsuite/birdsuite_pipeline.py
src/birdsuite/birdsuite_qc.py
src/birdsuite/birdsuite_qc_report.py
src/birdsuite/birdsuite_report.py
src/birdsuite/call_confidence_parser.py
src/birdsuite/calls_confidences_filter.py
src/birdsuite/cn_annotate_allele_summary.py
src/birdsuite/cn_create_exclude_list.py
src/birdsuite/cn_create_illumnia_exclude_list.py
src/birdsuite/cn_create_target.py
src/birdsuite/cn_locus_summarize.py
src/birdsuite/cn_probeset_summarize.py
src/birdsuite/cn_sample_dev.py
src/birdsuite/cn_select_autosomal_probes_for_normalization.py
src/birdsuite/cnv_definition_collection.py
src/birdsuite/compare_calls.py
src/birdsuite/enhance_ccs_ref_calls.py
src/birdsuite/filter_calls.py
src/birdsuite/find_birdseye_call.py
src/birdsuite/het_call_rate.py
src/birdsuite/initializeCNGaussians.py
src/birdsuite/make_cn_probe_locus_file.py
src/birdsuite/make_cnv_probe_map.py
src/birdsuite/make_guidefile.py
src/birdsuite/make_ped_and_map_file.py
src/birdsuite/make_special_cn_probes.py
src/birdsuite/medpolish.py
src/birdsuite/mendel_check.py
src/birdsuite/mendel_errors_by_chromosome.py
src/birdsuite/merge_birdsuite_plink_qc.py
src/birdsuite/merge_canary_reference_calls.py
src/birdsuite/plink_summarize_by_population.py
src/birdsuite/post_birdseye.py
src/birdsuite/pre_birdseye.py
src/birdsuite/run_plink_population.py
src/canarypriors/__init__.py
src/canarypriors/prep_clusters.py
src/curategenotypes/__init__.py
src/curategenotypes/curate.py
src/curategenotypes/curateCanaryGenotypes.py
src/curategenotypes/curate_test.py
src/curategenotypes/genotypeColors.py
src/curategenotypes/scatter.py
src/hapmap3/__init__.py
src/hapmap3/extract_intensity_sanger_format.py
src/hapmap3/sangerFormat_to_annotatedSummary.py
src/hapmap3/summarize_regions.py
src/metadataprocessing/__init__.py
src/metadataprocessing/merge_science_map.py
src/metadataprocessing/merge_smart_probes.py
src/metadataprocessing/segregate_probes_in_cnvs.py
src/optimizer/optimize_birdseed.py
src/optimizer/optimize_birdseed_params.py
src/optimizer/param_values.py
src/plink_pipeline/__init__.py
src/plink_pipeline/birdseye_merger.py
src/plink_pipeline/birdseye_to_cnv.py
src/plink_pipeline/birdsuite_to_plink.py
src/plink_pipeline/canary_to_gvar.py
src/plink_pipeline/create_map.py
src/plink_pipeline/diploid_calls_filter.py
src/plink_pipeline/fam_to_gender.py
src/plink_pipeline/fawkes_merge.py
src/plink_pipeline/fawkes_to_diploid.py
src/plink_pipeline/fawkes_to_gvar.py
src/plink_pipeline/make_tfam.py
src/plink_pipeline/make_tped.py
src/plink_pipeline/remove_common_cnvs.py
src/plinkpipeline.egg-info/PKG-INFO
src/plinkpipeline.egg-info/SOURCES.txt
src/plinkpipeline.egg-info/dependency_links.txt
src/plinkpipeline.egg-info/entry_points.txt
src/plinkpipeline.egg-info/requires.txt
src/plinkpipeline.egg-info/top_level.txt
test/Makefile
test/test_calc_callrate_stats/calc_callrate_statstest.py
test/test_calc_callrate_stats/expected/hapmap.txt
test/test_calc_callrate_stats/expected/hapmap_duplicates.txt
test/test_calc_callrate_stats/expected/perclustersize.txt
test/test_calc_callrate_stats/expected/persample.txt
test/test_calc_callrate_stats/expected/persnp.txt
test/test_calc_callrate_stats/expected/samplesubset_hapmap.txt
test/test_calc_callrate_stats/expected/samplesubset_hapmap_duplicates.txt
test/test_calc_callrate_stats/expected/samplesubset_perclustersize.txt
test/test_calc_callrate_stats/expected/samplesubset_persample.txt
test/test_calc_callrate_stats/expected/samplesubset_persnp.txt
test/test_calc_callrate_stats/expected/samplesubset_summary.txt
test/test_calc_callrate_stats/expected/summary.txt
test/test_calc_callrate_stats/input/calls.txt
test/test_calc_callrate_stats/input/confs.txt
test/test_calc_callrate_stats/input/guide.txt
test/test_calc_callrate_stats/input/guide_with_dupes.txt
test/test_calc_callrate_stats/input/samples.txt
test/test_cn_probeset_summarize/cn_probeset_summarizetest.py
test/test_cn_probeset_summarize/expected/medpolish-exp.bi.txt
test/test_cn_probeset_summarize/expected/medpolish-exp.normalize.txt
test/test_cn_probeset_summarize/expected/medpolish-exp.txt
test/test_cn_probeset_summarize/expected/medpolish.ignore-snps.txt
test/test_cn_probeset_summarize/expected/medpolish.txt
test/test_cn_probeset_summarize/expected/overlap.txt
test/test_cn_probeset_summarize/expected/rescale-median.txt
test/test_cn_probeset_summarize/input/bi_smart_cnp_defs.txt
test/test_cn_probeset_summarize/input/cnp_defs.txt
test/test_cn_probeset_summarize/input/cnp_defs_with_overlap.txt
test/test_cn_probeset_summarize/input/locus.txt
test/test_cn_probeset_summarize/input/normalization_probes.txt
test/test_cn_probeset_summarize/input/smart_cnp_defs.txt
test/test_cn_probeset_summarize/input/smart_cnp_defs_with_overlap.txt
test/test_mendel_check/mendel_checktest.py
test/test_mendel_check/expected/birdseed.imendel
test/test_mendel_check/expected/birdseed.lmendel
test/test_mendel_check/expected/birdseed.mendel
test/test_mendel_check/expected/canary.imendel
test/test_mendel_check/expected/canary.lmendel
test/test_mendel_check/expected/canary.mendel
test/test_mendel_check/expected/hwe.hwe
test/test_mendel_check/expected/hwe.imendel
test/test_mendel_check/expected/hwe.lmendel
test/test_mendel_check/expected/hwe.mendel
test/test_mendel_check/expected/larry_bird.hwe
test/test_mendel_check/expected/larry_bird.imendel
test/test_mendel_check/expected/larry_bird.lmendel
test/test_mendel_check/expected/larry_bird.mendel
test/test_mendel_check/expected/sample_subset.imendel
test/test_mendel_check/expected/sample_subset.lmendel
test/test_mendel_check/expected/sample_subset.mendel
test/test_mendel_check/input/birdseed.calls
test/test_mendel_check/input/birdseed.confs
test/test_mendel_check/input/birdseed.tfam
test/test_mendel_check/input/canary.calls
test/test_mendel_check/input/canary.confs
test/test_mendel_check/input/canary.special_probes
test/test_mendel_check/input/canary.tfam
test/test_mendel_check/input/hwe.calls
test/test_mendel_check/input/hwe.confs
test/test_mendel_check/input/hwe.tfam
test/test_mendel_check/input/larry_bird.calls
test/test_mendel_check/input/larry_bird.confs
test/test_mendel_check/input/larry_bird.tfam
test/test_mendel_check/input/sample_subset.calls
test/test_mendel_check/input/sample_subset.confs
test/test_mendel_check/input/sample_subset.samples
test/test_mendel_check/input/sample_subset.tfam
test/test_mendel_check/input/test.special_probes