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docs/delineate/delineate_HIW.rst
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docs/delineate/delineate_examples.rst
docs/delineate/delineate_faq.rst
docs/delineate/delineate_feature_definition.rst
docs/delineate/delineate_scope_usage.rst
docs/delineate/index.rst
docs/design/design_HIW.rst
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docs/images/sites/SMAP_haplotype_step2_Shotgun.png
docs/images/sites/SMAP_haplotype_step2_Shotgun_SNP.png
docs/images/sites/SMAP_haplotype_step2_Shotgun_SV.png
docs/images/sites/SMAP_haplotype_step3.png
docs/images/sites/SMAP_haplotype_step3_AS.png
docs/images/sites/SMAP_haplotype_step3_Shotgun.png
docs/images/sites/SMAP_haplotype_step4_Shotgun.png
docs/images/sites/SMAP_haplotype_step4b.png
docs/images/sites/SMAP_haplotype_step4b_ind.png
docs/images/sites/SMAP_haplotype_step5_Shotgun.png
docs/images/sites/SMAP_haplotype_step6.png
docs/images/sites/SMAP_haplotype_tetraploid_ind_read_count_requirement.png
docs/images/sites/SMAP_sites_introduction_scheme.png
docs/images/sites/Sample1_haplo_AS.png
docs/images/sites/Sample1_haplo_Shotgun_SNP_60bp.png
docs/images/sites/Sample1_haplo_Shotgun_SNP_non-overlappingFrames_40bp.png
docs/images/sites/Sample1_haplo_Shotgun_SNP_overlappingFrames.png
docs/images/sites/Sample2_haplo_AS.png
docs/images/sites/Sample2_haplo_Shotgun_SNP_60bp.png
docs/images/sites/Sample3_haplo_AS.png
docs/images/sites/Sample3_haplo_Shotgun_SNP_60bp.png
docs/images/sites/coordinates_GBS_manual.png
docs/images/sites/coordinates_HiPlex_manual.png
docs/images/sites/coordinates_Shotgun_SNP_short.png
docs/images/sites/coordinates_Shotgun_SNPs_manual.png
docs/images/sites/coordinates_Shotgun_SV_manual.png
docs/images/sites/coordinates_Shotgun_SV_short.png
docs/images/sites/dosage_filter_2n.png
docs/images/sites/dosage_filter_4n.png
docs/images/sites/formula_diploid_1.png
docs/images/sites/formula_diploid_2.png
docs/images/sites/formula_diploid_3.png
docs/images/sites/formula_tetraploid.png
docs/images/sites/haplotype_counts.cigar.barplot.png
docs/images/sites/haplotype_step_scheme_1-3.png
docs/images/sites/haplotype_step_scheme_1-6.png
docs/images/sites/haplotype_step_scheme_4-6.png
docs/images/sites/locus_call_completeness_correctness_40canephora.png
docs/images/sites/locus_definition_HiPlex_shotgun_SNPs.png
docs/images/sites/locus_definition_shotgun_SVs_GBS.png
docs/images/sites/sample_call_completeness_correctness_40canephora.png
docs/images/sites/scaffold_10030_Sample1_haplo_new.png
docs/images/sites/scaffold_10030_Sample2_haplo_new.png
docs/images/sites/scaffold_10030_Sample3_haplo_new.png
docs/images/sites/scaffold_10030_Sample4_haplo_new.png
docs/images/sites/scaffold_10030_Sample5_haplo_new.png
docs/images/sites/scaffold_10030_ref0030940_0070_edit.png
docs/images/utilities/SMAP_utilities_Sliding_frame_scope_Shotgun.png
docs/images/utilities/sliding_frames_probe_capture_graph1.png
docs/images/utilities/sliding_frames_probe_capture_graph2.png
docs/images/utilities/sliding_frames_probe_capture_graph3.png
docs/images/utilities/sliding_frames_probe_capture_graph4.png
docs/images/utilities/utilities_HIW_SNP_step1.png
docs/images/utilities/utilities_HIW_SNP_step2.png
docs/images/utilities/utilities_HIW_SNP_step3.png
docs/images/utilities/utilities_HIW_SNP_step4.png
docs/images/utilities/utilities_HIW_SNP_step6.png
docs/images/utilities/utilities_Sample1_40bp_SNPs.png
docs/images/utilities/utilities_Sample1_60bp_SNPs.png
docs/images/utilities/utilities_Sample1_RB_deletion.png
docs/images/utilities/utilities_Sample2_40bp_SNPs.png
docs/images/utilities/utilities_Sample2_60bp_SNPs.png
docs/images/utilities/utilities_Sample2_LB_deletion.png
docs/images/utilities/utilities_Sample2_short_deletion.png
docs/images/utilities/utilities_Sample3_40bp_SNPs.png
docs/images/utilities/utilities_Sample3_60bp_SNPs.png
docs/images/utilities/utilities_Sliding_frames_SNPs.png
docs/quickstart/index.rst
docs/quickstart/quickstart.rst
docs/sites/index.rst
docs/sites/sites_code.rst
docs/sites/sites_examples.rst
docs/sites/sites_rec_HIW.rst
docs/sites/sites_scope_usage.rst
docs/sites/LibraryPrep/index.rst
docs/sites/LibraryPrep/sites_GBS_HIW.rst
docs/sites/LibraryPrep/sites_HiPlex_HIW.rst
docs/sites/LibraryPrep/sites_Shotgun_HIW.rst
docs/sites/SampleType/index.rst
docs/sites/SampleType/sites_individuals_HIW.rst
docs/sites/SampleType/sites_pools_HIW.rst
docs/tables/design/WNK_CRISPOR_gRNA.csv
docs/tables/design/WNK_FlashFry_gRNA.csv
docs/tables/design/WNK_MITOOF_gRNA.csv
docs/tables/design/WNK_MITdoenchOOFoffTargets_gRNA.csv
docs/tables/design/WNK_NoScores_gRNA.csv
docs/tables/design/WNK_SMAPdesign_gRNAs.csv
docs/tables/design/WNK_SMAPdesign_gff.csv
docs/tables/design/WNK_SMAPdesign_primers.csv
docs/tables/design/WNK_SMAPdesign_summary.csv
docs/tables/design/WNK_offTargets_gRNA.csv
docs/tables/design/gene_families_data_file.csv
docs/tables/design/hom_groups.csv
docs/tables/design/test.csv
docs/tables/sites/2n_ind_GBS_SE_NI_DOSdiplo_FR_R10_F0.csv
docs/tables/sites/2n_ind_GBS_SE_NI_DOSdiplo_FR_R10_F1.csv
docs/tables/sites/2n_ind_GBS_SE_NI_DOSdiplo_FR_R10_F5.csv
docs/tables/sites/2n_ind_GBS_SE_NI_DOSdiplo_FR_R10_F5_M1.csv
docs/tables/sites/2n_ind_GBS_SE_NI_DOSdiplo_FR_R10_F5_M5.csv
docs/tables/sites/2n_ind_GBS_SE_haplo_call_f0.csv
docs/tables/sites/2n_ind_GBS_SE_haplo_call_f1.csv
docs/tables/sites/2n_ind_GBS_SE_haplo_call_f5.csv
docs/utilities/index.rst
docs/utilities/utilities_scope_usage.rst
ngs_smap.egg-info/PKG-INFO
ngs_smap.egg-info/SOURCES.txt
ngs_smap.egg-info/dependency_links.txt
ngs_smap.egg-info/entry_points.txt
ngs_smap.egg-info/requires.txt
ngs_smap.egg-info/top_level.txt
smap/__init__.py
smap/__main__.py
smap/__version__.py
smap/compare.py
smap/delineate.py
smap/grm.py
smap/haplotype.py
smap/plotting.py
test/data.py
test/test_compare.py
test/test_delineate.py
test/test_grm.py
test/test_haplotype.py
test/test_integration.py
utilities/SMAPutil_SlidingFrames.py