.coveragerc
.git_archival
.gitattributes
.gitignore
.gitlab-ci.yml
.pre-commit-config.yaml
.readthedocs.yaml
LICENSE
README.md
pyproject.toml
setup.cfg
docs/Makefile
docs/conf.py
docs/index.rst
docs/manual_index.txt
docs/images/SMAP_global_overview_sites.png
docs/images/SMAP_global_overview_sites_window_design.png
docs/images/SMAP_global_overview_sites_window_design_effect.png
docs/images/window/SMAP_global_overview_sites.png
docs/images/window/SMAP_haplotype_diploid_ind_read_count_requirement.png
docs/images/window/SMAP_haplotype_window_SQS_short.png
docs/images/window/SMAP_window_crispr_1.png
docs/images/window/SMAP_window_crispr_2.png
docs/images/window/SMAP_window_crispr_3.png
docs/images/window/SMAP_window_crispr_4.png
docs/images/window/SMAP_window_crispr_5.png
docs/images/window/SMAP_window_crispr_6.png
docs/images/window/SMAP_window_crispr_7.png
docs/images/window/SMAP_window_crispr_8.png
docs/images/window/SMAP_window_design_1.png
docs/images/window/SMAP_window_step1_AS.png
docs/images/window/SMAP_window_step1_SS.png
docs/images/window/SMAP_window_step2_AS.png
docs/images/window/SMAP_window_step2_AS_new.png
docs/images/window/SMAP_window_step2_SS.png
docs/images/window/SMAP_window_step2_SS_new.png
docs/images/window/SMAP_window_step3_AS.png
docs/images/window/SMAP_window_step3_AS_new.png
docs/images/window/SMAP_window_step4b.png
docs/images/window/SMAP_window_step4b_ind.png
docs/images/window/SMAP_window_step4b_new.png
docs/images/window/SMAP_window_step6.png
docs/images/window/Sample1_window_bam_AS.png
docs/images/window/Sample1_window_bam_SS.png
docs/images/window/Sample2_window_bam_AS.png
docs/images/window/Sample2_window_bam_SS.png
docs/images/window/Sample3_window_bam_AS.png
docs/images/window/Sample3_window_bam_SS.png
docs/images/window/dosage_mask_2n.png
docs/images/window/dosage_mask_4n.png
docs/images/window/formula_diploid_1.png
docs/images/window/formula_diploid_2.png
docs/images/window/formula_diploid_3.png
docs/images/window/formula_tetraploid.png
docs/images/window/haplotype_step_scheme_34.png
docs/images/window/haplotype_window_scheme.png
docs/images/window/haplotype_window_scheme2.png
docs/images/window/haplotype_window_scheme_short.png
docs/images/window/haplotype_window_scheme_short_TR_all.png
docs/images/window/haplotype_window_shotgun_window_size_100.png
docs/images/window/haplotype_window_shotgun_window_size_80.png
docs/images/window/haplotype_window_step_scheme.png
docs/images/window/haplotype_window_step_scheme_12.png
docs/images/window/smap_window_sgrna_extraction_crispr.png
docs/images/window/window_bam_2_fastq_AS.png
docs/images/window/window_bam_2_fastq_SS.png
docs/images/window/window_bam_to_fastq_AS.png
docs/images/window/window_sliding_window_concept.png
docs/tables/window/crispr_example_sorted.csv
docs/tables/window/crispr_example_unsorted.csv
docs/tables/window/example_HiPlex_gff.csv
docs/tables/window/example_Shotgun_gff.csv
docs/window/index.rst
docs/window/window_code.rst
docs/window/window_crispr.rst
docs/window/window_gff_sliding_window.rst
docs/window/window_rec_HIW.rst
docs/window/window_scope_quickstart.rst
docs/window/LibraryPrep/index.rst
docs/window/LibraryPrep/window_HiPlex_HIW.rst
docs/window/LibraryPrep/window_Shotgun_HIW.rst
docs/window/SampleType/index.rst
docs/window/SampleType/window_individuals_HIW.rst
docs/window/SampleType/window_pools_HIW.rst
smap_haplotype_window.egg-info/PKG-INFO
smap_haplotype_window.egg-info/SOURCES.txt
smap_haplotype_window.egg-info/dependency_links.txt
smap_haplotype_window.egg-info/entry_points.txt
smap_haplotype_window.egg-info/requires.txt
smap_haplotype_window.egg-info/top_level.txt
smap_window/__init__.py
smap_window/arguments.py
smap_window/haplotype_window.py
smap_window/version.py
test/__init__.py
test/sample_files.py
test/test_window.py