From 4380d3c41c8d326c4b4c4dfe62c7819f567c7ff2 Mon Sep 17 00:00:00 2001 From: jamesli124 <58196853+jamesli124@users.noreply.github.com> Date: Tue, 14 Jan 2025 17:03:47 -0500 Subject: [PATCH] update docs --- .../api_reference/basicfeatures.doctree | Bin 91247 -> 90956 bytes .../api_reference/cleavageprofile.doctree | Bin 32112 -> 30431 bytes .../documentation/api_reference/delfi.doctree | Bin 43586 -> 44920 bytes .../api_reference/endmotifs.doctree | Bin 183509 -> 182193 bytes .../api_reference/fragfile.doctree | Bin 140206 -> 136818 bytes .../api_reference/genomeutils.doctree | Bin 80902 -> 80099 bytes .../documentation/api_reference/index.doctree | Bin 3091 -> 3094 bytes .../documentation/api_reference/wps.doctree | Bin 101673 -> 98876 bytes .../documentation/cli_reference/index.doctree | Bin 256599 -> 246888 bytes .../doctrees/documentation/index.doctree | Bin 3135 -> 3138 bytes .../documentation/user_guide/features.doctree | Bin 11889 -> 11892 bytes .../documentation/user_guide/help.doctree | Bin 5453 -> 5456 bytes .../documentation/user_guide/index.doctree | Bin 3132 -> 3135 bytes .../user_guide/inputdata.doctree | Bin 11467 -> 11470 bytes .../user_guide/installation.doctree | Bin 6495 -> 6498 bytes .../user_guide/intersectpolicy.doctree | Bin 6574 -> 6577 bytes .../user_guide/quickstart.doctree | Bin 7664 -> 7667 bytes .../user_guide/structure.doctree | Bin 4884 -> 4887 bytes .../documentation/user_guide/what.doctree | Bin 5367 -> 5370 bytes docs/_build/doctrees/environment.pickle | Bin 94767 -> 94107 bytes docs/_build/doctrees/index.doctree | Bin 15968 -> 15941 bytes docs/_build/html/.buildinfo | 4 +- docs/_build/html/_static/basic.css | 15 +- docs/_build/html/_static/doctools.js | 7 + docs/_build/html/_static/language_data.js | 7 + docs/_build/html/_static/pygments.css | 242 +++++++------- docs/_build/html/_static/searchtools.js | 38 +-- .../api_reference/basicfeatures.html | 12 +- .../api_reference/cleavageprofile.html | 8 +- .../documentation/api_reference/delfi.html | 8 +- .../api_reference/endmotifs.html | 12 +- .../documentation/api_reference/fragfile.html | 8 +- .../api_reference/genomeutils.html | 6 +- .../documentation/api_reference/index.html | 6 +- .../html/documentation/api_reference/wps.html | 10 +- .../documentation/cli_reference/index.html | 298 +++++++++--------- docs/_build/html/documentation/index.html | 6 +- .../documentation/user_guide/features.html | 6 +- .../html/documentation/user_guide/help.html | 6 +- .../html/documentation/user_guide/index.html | 6 +- .../documentation/user_guide/inputdata.html | 6 +- .../user_guide/installation.html | 6 +- .../user_guide/intersectpolicy.html | 6 +- .../documentation/user_guide/quickstart.html | 10 +- .../documentation/user_guide/structure.html | 6 +- .../html/documentation/user_guide/what.html | 6 +- docs/_build/html/genindex.html | 6 +- docs/_build/html/index.html | 10 +- docs/_build/html/search.html | 6 +- docs/_build/html/searchindex.js | 2 +- 50 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When it is not found, a full rebuild will be done. -config: a6a7c49fe85dc34358516258c905dd38 +# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 670efaa449e3fccfe64f8fb2cf4a7d46 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/_static/basic.css b/docs/_build/html/_static/basic.css index 7ebbd6d0..f316efcb 100644 --- a/docs/_build/html/_static/basic.css +++ b/docs/_build/html/_static/basic.css @@ -1,5 +1,12 @@ /* + * basic.css + * ~~~~~~~~~ + * * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * */ /* -- main layout ----------------------------------------------------------- */ @@ -108,11 +115,15 @@ img { /* -- search page ----------------------------------------------------------- */ ul.search { - margin-top: 10px; + margin: 10px 0 0 20px; + padding: 0; } ul.search li { - padding: 5px 0; + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; } ul.search li a { diff --git a/docs/_build/html/_static/doctools.js b/docs/_build/html/_static/doctools.js index 0398ebb9..4d67807d 100644 --- a/docs/_build/html/_static/doctools.js +++ b/docs/_build/html/_static/doctools.js @@ -1,5 +1,12 @@ /* + * doctools.js + * ~~~~~~~~~~~ + * * Base JavaScript utilities for all Sphinx HTML documentation. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * */ "use strict"; diff --git a/docs/_build/html/_static/language_data.js b/docs/_build/html/_static/language_data.js index c7fe6c6f..367b8ed8 100644 --- a/docs/_build/html/_static/language_data.js +++ b/docs/_build/html/_static/language_data.js @@ -1,6 +1,13 @@ /* + * language_data.js + * ~~~~~~~~~~~~~~~~ + * * This script contains the language-specific data used by searchtools.js, * namely the list of stopwords, stemmer, scorer and splitter. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * */ var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; diff --git a/docs/_build/html/_static/pygments.css b/docs/_build/html/_static/pygments.css index d7dd5778..012e6a00 100644 --- a/docs/_build/html/_static/pygments.css +++ b/docs/_build/html/_static/pygments.css @@ -6,11 +6,11 @@ html[data-theme="light"] .highlight span.linenos.special { color: #000000; backg html[data-theme="light"] .highlight .hll { background-color: #fae4c2 } html[data-theme="light"] .highlight { background: #fefefe; color: #080808 } html[data-theme="light"] .highlight .c { color: #515151 } /* Comment */ -html[data-theme="light"] .highlight .err { color: #A12236 } /* Error */ -html[data-theme="light"] .highlight .k { color: #6730C5 } /* Keyword */ -html[data-theme="light"] .highlight .l { color: #7F4707 } /* Literal 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color: #abe338 } /* Literal.String.Other */ +html[data-theme="dark"] .highlight .sr { color: #ffa07a } /* Literal.String.Regex */ +html[data-theme="dark"] .highlight .s1 { color: #abe338 } /* Literal.String.Single */ +html[data-theme="dark"] .highlight .ss { color: #00e0e0 } /* Literal.String.Symbol */ +html[data-theme="dark"] .highlight .bp { color: #ffd900 } /* Name.Builtin.Pseudo */ +html[data-theme="dark"] .highlight .fm { color: #00e0e0 } /* Name.Function.Magic */ +html[data-theme="dark"] .highlight .vc { color: #ffa07a } /* Name.Variable.Class */ +html[data-theme="dark"] .highlight .vg { color: #ffa07a } /* Name.Variable.Global */ +html[data-theme="dark"] .highlight .vi { color: #ffa07a } /* Name.Variable.Instance */ +html[data-theme="dark"] .highlight .vm { color: #ffd900 } /* Name.Variable.Magic */ +html[data-theme="dark"] .highlight .il { color: #ffd900 } /* Literal.Number.Integer.Long */ \ No newline at end of file diff --git a/docs/_build/html/_static/searchtools.js b/docs/_build/html/_static/searchtools.js index 2c774d17..b08d58c9 100644 --- a/docs/_build/html/_static/searchtools.js +++ b/docs/_build/html/_static/searchtools.js @@ -1,5 +1,12 @@ /* + * searchtools.js + * ~~~~~~~~~~~~~~~~ + * * Sphinx JavaScript utilities for the full-text search. + * + * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * */ "use strict"; @@ -13,7 +20,7 @@ if (typeof Scorer === "undefined") { // and returns the new score. /* score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result + const [docname, title, anchor, descr, score, filename] = result return score }, */ @@ -40,14 +47,6 @@ if (typeof Scorer === "undefined") { }; } -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - const _removeChildren = (element) => { while (element && element.lastChild) element.removeChild(element.lastChild); }; @@ -65,13 +64,9 @@ const _displayItem = (item, searchTerms, highlightTerms) => { const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; const contentRoot = document.documentElement.dataset.content_root; - const [docName, title, anchor, descr, score, _filename, kind] = item; + const [docName, title, anchor, descr, score, _filename] = item; let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); let requestUrl; let linkUrl; if (docBuilder === "dirhtml") { @@ -120,10 +115,8 @@ const _finishSearch = (resultCount) => { "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." ); else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( @@ -145,7 +138,7 @@ const _displayNextItem = ( else _finishSearch(resultCount); }; // Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Each input is an array of [docname, title, anchor, descr, score, filename]. // Order the results by score (in opposite order of appearance, since the // `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. const _orderResultsByScoreThenName = (a, b) => { @@ -255,7 +248,6 @@ const Search = { searchSummary.classList.add("search-summary"); searchSummary.innerText = ""; const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); searchList.classList.add("search"); const out = document.getElementById("search-results"); @@ -326,7 +318,7 @@ const Search = { const indexEntries = Search._index.indexentries; // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + // Each is an array of [docname, title, anchor, descr, score, filename]. const normalResults = []; const nonMainIndexResults = []; @@ -345,7 +337,6 @@ const Search = { null, score + boost, filenames[file], - SearchResultKind.title, ]); } } @@ -363,7 +354,6 @@ const Search = { null, score, filenames[file], - SearchResultKind.index, ]; if (isMain) { normalResults.push(result); @@ -485,7 +475,6 @@ const Search = { descr, score, filenames[match[0]], - SearchResultKind.object, ]); }; Object.keys(objects).forEach((prefix) => @@ -596,7 +585,6 @@ const Search = { null, score, filenames[file], - SearchResultKind.text, ]); } return results; diff --git a/docs/_build/html/documentation/api_reference/basicfeatures.html b/docs/_build/html/documentation/api_reference/basicfeatures.html index 9c168def..2ed2238d 100644 --- a/docs/_build/html/documentation/api_reference/basicfeatures.html +++ b/docs/_build/html/documentation/api_reference/basicfeatures.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -362,7 +362,7 @@

Basic Features#

-finaletoolkit.frag.coverage(input_file: str | TabixFile | AlignmentFile | Path, interval_file: str, output_file: str, scale_factor: float = 1.0, min_length: int | None = None, max_length: int | None = None, normalize: bool = False, intersect_policy: str = 'midpoint', quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False) → list[tuple[str, int, int, str, float]]#
+finaletoolkit.frag.coverage(input_file: str | pysam.TabixFile | pysam.AlignmentFile | Path, interval_file: str, output_file: str, scale_factor: float = 1.0, min_length: int | None = None, max_length: int | None = None, normalize: bool = False, intersect_policy: str = 'midpoint', quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False) → list[tuple[str, int, int, str, float]]#

Return estimated fragment coverage over intervals specified in intervals. Fragments are read from input_file which may be a BAM, CRAM, or fragment file. Uses an algorithm where the @@ -404,7 +404,7 @@

Basic Features
-finaletoolkit.frag.frag_length(input_file: str | AlignmentFile | TabixFile, contig: str | None = None, start: int | None = None, stop: int | None = None, intersect_policy: str = 'midpoint', output_file: str | None = None, quality_threshold: int = 30, verbose: bool = False) → ndarray#
+finaletoolkit.frag.frag_length(input_file: str | pysam.AlignmentFile | pysam.TabixFile, contig: str | None = None, start: int | None = None, stop: int | None = None, intersect_policy: str = 'midpoint', output_file: str | None = None, quality_threshold: int = 30, verbose: bool = False) → np.ndarray#

Return np.ndarray containing lengths of fragments in input_file that are above the quality threshold and are proper-paired reads.

@@ -437,7 +437,7 @@

Basic Features
-finaletoolkit.frag.frag_length_bins(input_file: str | AlignmentFile, contig: str | None = None, start: int | None = None, stop: int | None = None, min_length: int | None = 0, max_length: int | None = None, bin_size: int = 1, output_file: str | None = None, intersect_policy: str = 'midpoint', quality_threshold: int = 30, histogram_path: str | None = None, verbose: bool | int = False) → tuple[ndarray, ndarray]#
+finaletoolkit.frag.frag_length_bins(input_file: str | pysam.AlignmentFile, contig: str | None = None, start: int | None = None, stop: int | None = None, min_length: int | None = 0, max_length: int | None = None, bin_size: int = 1, output_file: str | None = None, intersect_policy: str = 'midpoint', quality_threshold: int = 30, histogram_path: str | None = None, verbose: bool | int = False) → tuple[np.ndarray, np.ndarray]#

Takes input_file, computes frag lengths of fragments and returns two arrays containing bins and counts by size. Optionally prints data to output as a tab delimited table or histogram.

@@ -566,7 +566,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/cleavageprofile.html b/docs/_build/html/documentation/api_reference/cleavageprofile.html index 0a1941ab..f66959e4 100644 --- a/docs/_build/html/documentation/api_reference/cleavageprofile.html +++ b/docs/_build/html/documentation/api_reference/cleavageprofile.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -362,7 +362,7 @@

Cleavage Profile#

-finaletoolkit.frag.cleavage_profile(input_file: str | PathLike | AlignmentFile | TabixFile, chrom_size: int, contig: str, start: int, stop: int, left: int = 0, right: int = 0, min_length: int | None = None, max_length: int | None = None, quality_threshold: int = 30, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None) → ndarray#
+finaletoolkit.frag.cleavage_profile(input_file: FragFile, chrom_size: int, contig: str, start: int, stop: int, left: int = 0, right: int = 0, min_length: int | None = None, max_length: int | None = None, quality_threshold: int = 30, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None) → np.ndarray#

Cleavage profile calculated over a single interval.

Parameters:
@@ -488,7 +488,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/delfi.html b/docs/_build/html/documentation/api_reference/delfi.html index 3a70b718..827323ff 100644 --- a/docs/_build/html/documentation/api_reference/delfi.html +++ b/docs/_build/html/documentation/api_reference/delfi.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -362,7 +362,7 @@

DELFI#

-finaletoolkit.frag.delfi(input_file: str, chrom_sizes: str, bins_file: str, reference_file: str, blacklist_file: str = None, gap_file: str | GenomeGaps = None, output_file: str = None, gc_correct: bool = True, remove_nocov: bool = True, merge_bins: bool = True, window_size: int = 5000000, quality_threshold: int = 30, workers: int = 1, verbose: int | bool = False) → DataFrame#
+finaletoolkit.frag.delfi(input_file: str, chrom_sizes: str, bins_file: str, reference_file: str, blacklist_file: str | None = None, gap_file: str | GenomeGaps | None = None, output_file: str | None = None, gc_correct: bool = True, remove_nocov: bool = True, merge_bins: bool = True, window_size: int = 5000000, quality_threshold: int = 30, workers: int = 1, verbose: int | bool = False) → DataFrame#

A function that replicates the methodology of Christiano et al (2019).

@@ -519,7 +519,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/endmotifs.html b/docs/_build/html/documentation/api_reference/endmotifs.html index 4ffc3b42..43b6d80b 100644 --- a/docs/_build/html/documentation/api_reference/endmotifs.html +++ b/docs/_build/html/documentation/api_reference/endmotifs.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -377,7 +377,7 @@

End-Motifs
-classmethod from_file(file_path: str | Path, quality_threshold: int, sep: str = '\t', header: int = 0) → EndMotifFreqs#
+classmethod from_file(file_path: str | Path, quality_threshold: int, sep: str = '\t', header: int = 0) → EndMotifFreqs#

Reads kmer frequency from a two-column tab-delimited file.

Parameters:
@@ -565,7 +565,7 @@

End-Motifs
-finaletoolkit.frag.end_motifs(input_file: str, refseq_file: str | Path, k: int = 4, min_length: int = 10, max_length: int = 600, both_strands: bool = True, negative_strand: bool = False, output_file: None | str = None, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False, fraction_low: int | None = None, fraction_high: int | None = None) → EndMotifFreqs#
+finaletoolkit.frag.end_motifs(input_file: str, refseq_file: str | Path, k: int = 4, min_length: int = 10, max_length: int = 600, both_strands: bool = True, negative_strand: bool = False, output_file: None | str = None, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False, fraction_low: int | None = None, fraction_high: int | None = None) → EndMotifFreqs#

Function that reads fragments from a BAM, CRAM, or tabix indexed file and returns the 5’ k-mer (default is 4-mer) end motif frequencies as a dictionary. Optionally writes data to a tsv. This @@ -605,7 +605,7 @@

End-Motifs
-finaletoolkit.frag.interval_end_motifs(input_file: str, refseq_file: str | Path, intervals: str | Iterable[tuple[str, int, int, str]], k: int = 4, min_length: int | None = 10, max_length: int | None = 600, both_strands: bool = True, negative_strand: bool = False, output_file: str | None = None, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False, fraction_low: int | None = None, fraction_high: int | None = None) → EndMotifsIntervals#
+finaletoolkit.frag.interval_end_motifs(input_file: str, refseq_file: str | Path, intervals: str | Iterable[tuple[str, int, int, str]], k: int = 4, min_length: int | None = 10, max_length: int | None = 600, both_strands: bool = True, negative_strand: bool = False, output_file: str | None = None, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False, fraction_low: int | None = None, fraction_high: int | None = None) → EndMotifsIntervals#

Function that reads fragments from a BAM, CRAM, or tabix indexed file and user-specified intervals and returns the 5’ k-mer (default is 4-mer) end motif. Optionally writes data to a tsv.

@@ -752,7 +752,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/fragfile.html b/docs/_build/html/documentation/api_reference/fragfile.html index 5258675b..7858c849 100644 --- a/docs/_build/html/documentation/api_reference/fragfile.html +++ b/docs/_build/html/documentation/api_reference/fragfile.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -511,7 +511,7 @@

Frag File Utilities
-finaletoolkit.utils.frag_array(input_file: str | PathLike | AlignmentFile | TabixFile, contig: str, quality_threshold: int = 30, start: int | None = None, stop: int | None = None, min_length: int | None = None, max_length: int | None = None, intersect_policy: str = 'midpoint', verbose: bool = False) → ndarray[Any, dtype[_ScalarType_co]]#
+finaletoolkit.utils.frag_array(input_file: FragFile, contig: str, quality_threshold: int = 30, start: int | None = None, stop: int | None = None, min_length: int | None = None, max_length: int | None = None, intersect_policy: str = 'midpoint', verbose: bool = False) → NDArray#

Reads from BAM, CRAM, or fragment file and returns a three column matrix with fragment start and stop positions and strand.

@@ -684,7 +684,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/genomeutils.html b/docs/_build/html/documentation/api_reference/genomeutils.html index 86dd663d..72179329 100644 --- a/docs/_build/html/documentation/api_reference/genomeutils.html +++ b/docs/_build/html/documentation/api_reference/genomeutils.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -726,7 +726,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/index.html b/docs/_build/html/documentation/api_reference/index.html index e40dee31..ca4b4009 100644 --- a/docs/_build/html/documentation/api_reference/index.html +++ b/docs/_build/html/documentation/api_reference/index.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -494,7 +494,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/wps.html b/docs/_build/html/documentation/api_reference/wps.html index b3476e11..abe1de2d 100644 --- a/docs/_build/html/documentation/api_reference/wps.html +++ b/docs/_build/html/documentation/api_reference/wps.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -362,7 +362,7 @@

Window Protection Score (WPS)#

-finaletoolkit.frag.wps(input_file: str | AlignmentFile, chrom: str, start: int, stop: int, chrom_size: int, output_file: str | None = None, window_size: int = 120, min_length: int = 120, max_length: int = 180, quality_threshold: int = 30, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None) → ndarray#
+finaletoolkit.frag.wps(input_file: str | pysam.AlignmentFile, chrom: str, start: int, stop: int, chrom_size: int, output_file: str | None = None, window_size: int = 120, min_length: int = 120, max_length: int = 180, quality_threshold: int = 30, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None) → np.ndarray#

Return (raw) Windowed Protection Scores as specified in Snyder et al (2016) over a region [start,stop).

@@ -399,7 +399,7 @@

Window Protection Score (WPS)
-finaletoolkit.frag.multi_wps(input_file: str | PathLike | AlignmentFile | TabixFile, site_bed: str | PathLike, chrom_sizes: str | PathLike | None = None, output_file: str | None = None, window_size: int = 120, interval_size: int = 5000, min_length: int = 120, max_length: int = 180, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None)#
+finaletoolkit.frag.multi_wps(input_file: FragFile, site_bed: Intervals, chrom_sizes: ChromSizes | None = None, output_file: str | None = None, window_size: int = 120, interval_size: int = 5000, min_length: int = 120, max_length: int = 180, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None)#

Function that aggregates WPS over sites in BED file according to the method described by Snyder et al (2016).

@@ -572,7 +572,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/cli_reference/index.html b/docs/_build/html/documentation/cli_reference/index.html index bc4df73f..aaf7fda6 100644 --- a/docs/_build/html/documentation/cli_reference/index.html +++ b/docs/_build/html/documentation/cli_reference/index.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -355,8 +355,8 @@

CLI#

... -
-

Named Arguments#

+
+

Named Arguments#

-v, --version

show program’s version number and exit

@@ -368,7 +368,8 @@

Sub-commands

coverage#

Calculates fragmentation coverage over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.

-
finaletoolkit coverage [-h] [-o OUTPUT_FILE] [-n] [-s SCALE_FACTOR] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
+
finaletoolkit coverage [-h] [-o OUTPUT_FILE] [-n] [-s SCALE_FACTOR] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-q QUALITY_THRESHOLD]
+                       [-w WORKERS] [-v]
                        input_file interval_file
 

 

@@ -383,24 +384,24 @@ 
Positional Arguments

-
-

Named Arguments#

+
+

Named Arguments#

-o, --output-file

A BED file containing coverage values over the intervals specified in interval file.

-

Default: '-'

+

Default: “-”

-n, --normalize

If flag set, multiplies by user inputed scale factor if given and normalizes output by total coverage. May lead to longer execution time for high-throughput data.

-

Default: False

+

Default: False

-s, --scale-factor

Scale factor for coverage values. Default is 1.

-

Default: 1.0

+

Default: 1.0

-min, --min-length

Minimum length for a fragment to be included in coverage.

-

Default: 0

+

Default: 0

-max, --max-length

Maximum length for a fragment to be included in coverage.

@@ -408,19 +409,19 @@

Named Arguments'midpoint'

+

Default: “midpoint”

-q, --quality-threshold

Minimum mapping quality threshold.

-

Default: 30

+

Default: 30

-w, --workers

Number of worker processes.

-

Default: 1

+

Default: 1

-v, --verbose

Enable verbose mode to display detailed processing information.

-

Default: False

+

Default: False

@@ -428,8 +429,8 @@

Named Arguments

frag-length-bins#

Retrieves fragment lengths grouped in bins given a BAM/CRAM/Fragment file.

-
finaletoolkit frag-length-bins [-h] [-c CONTIG] [-S START] [-E STOP] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [--bin-size BIN_SIZE] [-o OUTPUT_FILE]
-                               [--histogram-path HISTOGRAM_PATH] [-q QUALITY_THRESHOLD] [-v]
+
finaletoolkit frag-length-bins [-h] [-c CONTIG] [-S START] [-E STOP] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [--bin-size BIN_SIZE]
+                               [-o OUTPUT_FILE] [--histogram-path HISTOGRAM_PATH] [-q QUALITY_THRESHOLD] [-v]
                                input_file
 

 

@@ -441,8 +442,8 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-c, --contig

 
Specify the contig or chromosome to select fragments from. (Required if using –start or –stop.)

@@ -455,7 +456,7 @@ 
Named Arguments0

+
Default: 0

 

 
-max, --max-length

 
Maximum length for a fragment to be included in fragment length.

@@ -463,26 +464,26 @@ 
Named Arguments'midpoint'

+
Default: “midpoint”

 

 
--bin-size

 
Specify the size of the bins to group fragment lengths into.

-
Default: 1

+
Default: 1

 

 
-o, --output-file

 
A .TSV file containing containing fragment lengths binned according to the specified bin size.

-
Default: '-'

+
Default: “-”

 

 
--histogram-path

 
Path to store histogram.

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 30

+
Default: 30

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -490,7 +491,8 @@ 
Named Arguments
 
frag-length-intervals#

 
Retrieves fragment length summary statistics over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.

-
finaletoolkit frag-length-intervals [-h] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v] input_file interval_file
+
finaletoolkit frag-length-intervals [-h] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
+                                    input_file interval_file
 

 

 

@@ -504,12 +506,12 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-min, --min-length

 
Minimum length for a fragment to be included in fragment length.

-
Default: 0

+
Default: 0

 

 
-max, --max-length

 
Maximum length for a fragment to be included in fragment length.

@@ -517,23 +519,23 @@ 
Named Arguments'midpoint'

+
Default: “midpoint”

 

 
-o, --output-file

 
A BED file containing fragment length summary statistics (mean, median, st. dev, min, max) over the intervals specified in the interval file.

-
Default: '-'

+
Default: “-”

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 30

+
Default: 30

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -541,8 +543,8 @@ 
Named Arguments
 
cleavage-profile#

 
Calculates cleavage proportion over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.

-
finaletoolkit cleavage-profile [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-q QUALITY_THRESHOLD] [-l LEFT] [-r RIGHT]
-                               [-w WORKERS] [-v]
+
finaletoolkit cleavage-profile [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH]
+                               [-q QUALITY_THRESHOLD] [-l LEFT] [-r RIGHT] [-w WORKERS] [-v]
                                input_file interval_file
 

 

@@ -557,19 +559,19 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-c, --chrom-sizes

 
A .chrom.sizes file containing chromosome names and sizes.

 

 
-o, --output-file

 
A bigWig file containing the cleavage proportion results over the intervals specified in interval file.

-
Default: '-'

+
Default: “-”

 

 
-min, --min-length

 
Minimum length for a fragment to be included.

-
Default: 0

+
Default: 0

 

 
-max, --max-length

 
Maximum length for a fragment to be included.

@@ -582,23 +584,23 @@ 
Named Arguments20

+
Default: 20

 

 
-l, --left

 
Number of base pairs to subtract from start coordinate to create interval. Useful when dealing with BED files with only CpG coordinates. Default is 0.

-
Default: 0

+
Default: 0

 

 
-r, --right

 
Number of base pairs to add to stop coordinate to create interval. Useful when dealing with BED files with only CpG coordinates. Default is 0.

-
Default: 0

+
Default: 0

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -606,8 +608,8 @@ 
Named Arguments
 
wps#

 
Calculates Windowed Protection Score (WPS) over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.

-
finaletoolkit wps [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-W WINDOW_SIZE] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-q QUALITY_THRESHOLD]
-                  [-w WORKERS] [-v]
+
finaletoolkit wps [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-W WINDOW_SIZE] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH]
+                  [-hi MAX_LENGTH] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
                   input_file site_bed
 

 

@@ -622,31 +624,31 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-c, --chrom-sizes

 
A .chrom.sizes file containing chromosome names and sizes.

 

 
-o, --output-file

 
A bigWig file containing the WPS results over the intervals specified in interval file.

-
Default: '-'

+
Default: “-”

 

 
-i, --interval-size

 
Size in bp of the intervals to calculate WPS over. Thesenew intervals are centered over those specified in the site_bed.Default is 5000

-
Default: 5000

+
Default: 5000

 

 
-W, --window-size

 
Size of the sliding window used to calculate WPS scores. Default is 120

-
Default: 120

+
Default: 120

 

 
-min, --min-length

 
Minimum length for a fragment to be included. Default is 120, corresponding to L-WPS.

-
Default: 120

+
Default: 120

 

 
-max, --max-length

 
Maximum length for a fragment to be included. Default is 180, corresponding to L-WPS.

-
Default: 180

+
Default: 180

 

 
-lo, --fraction_low

 
Minimum length for a fragment to be included in WPS calculation. Deprecated. Use –min-length instead.

@@ -656,15 +658,15 @@ 
Named Arguments30

+
Default: 30

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -672,8 +674,8 @@ 
Named Arguments
 
adjust-wps#

 
Adjusts raw Windowed Protection Score (WPS) by applying a median filter and Savitsky-Golay filter.

-
finaletoolkit adjust-wps [-h] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-m MEDIAN_WINDOW_SIZE] [-s SAVGOL_WINDOW_SIZE] [-p SAVGOL_POLY_DEG] [-S] [-w WORKERS] [--mean] [--subtract-edges]
-                         [--edge-size EDGE_SIZE] [-v]
+
finaletoolkit adjust-wps [-h] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-m MEDIAN_WINDOW_SIZE] [-s SAVGOL_WINDOW_SIZE] [-p SAVGOL_POLY_DEG] [-S] [-w WORKERS]
+                         [--mean] [--subtract-edges] [--edge-size EDGE_SIZE] [-v]
                          input_file interval_file chrom_sizes
 

 

@@ -691,48 +693,48 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-o, --output-file

 
A bigWig file containing the adjusted WPS results over the intervals specified in interval file.

-
Default: '-'

+
Default: “-”

 

 
-i, --interval_size

 
Size in bp of each interval in the interval file.

-
Default: 5000

+
Default: 5000

 

 
-m, --median-window-size

 
Size of the median filter or mean filter window used to adjust WPS scores.

-
Default: 1000

+
Default: 1000

 

 
-s, --savgol-window-size

 
Size of the Savitsky-Golay filter window used to adjust WPS scores.

-
Default: 21

+
Default: 21

 

 
-p, --savgol-poly-deg

 
Degree polynomial for Savitsky-Golay filter.

-
Default: 2

+
Default: 2

 

 
-S, --exclude-savgol

 
Do not perform Savitsky-Golay filteringscores.

-
Default: True

+
Default: True

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
--mean

 
A mean filter is used instead of median.

-
Default: False

+
Default: False

 

 
--subtract-edges

 
Take the median of the first and last 500 bases in a window and subtract from the whole interval.

-
Default: False

+
Default: False

 

 
--edge-size

 
size of the edge subtracted from ends of window when –subtract-edges is set. Default is 500.

-
Default: 500

+
Default: 500

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

@@ -764,8 +766,8 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-b, --blacklist-file

 
BED file containing regions to ignore when calculating DELFI.

@@ -775,35 +777,35 @@ 
Named Arguments'-'

+
Default: “-”

 

 
-G, --no-gc-correct

 
Skip GC correction.

-
Default: True

+
Default: True

 

 
-R, --keep-nocov

 
Skip removal two regions in hg19 with no coverage. Use this flag when not using hg19 human reference genome.

-
Default: True

+
Default: True

 

 
-M, --no-merge-bins

 
Keep 100kb bins and do not merge to 5Mb size.

-
Default: True

+
Default: True

 

 
-s, --window-size

 
Specify size of large genomic intervals to merge smaller 100kb intervals (or whatever the user specified in bins_file) into. Defaultis 5000000

-
Default: 5000000

+
Default: 5000000

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 30

+
Default: 30

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -822,16 +824,16 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-o, --output-file

 
BED to print GC-corrected DELFI fractions. If “-”, will write to stdout.

-
Default: '-'

+
Default: “-”

 

 
--header-lines

 
Number of header lines in BED.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

@@ -842,7 +844,8 @@ 
Named Arguments
 
end-motifs#

 
Measures frequency of k-mer 5’ end motifs.

-
finaletoolkit end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-B] [-n] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v] input_file refseq_file
+
finaletoolkit end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-B] [-n] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
+                         input_file refseq_file
 

 

 

@@ -856,43 +859,43 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-k

 
Length of k-mer.

-
Default: 4

+
Default: 4

 

 
-min, --min-length

 
Minimum length for a fragment to be included.

-
Default: 0

+
Default: 0

 

 
-max, --max-length

 
Maximum length for a fragment to be included.

 

 
-B, --no-both-strands

 
Set flag to only consider one strand for end-motifs.

-
Default: True

+
Default: True

 

 
-n, --negative-strand

 
Set flag in conjunction with -B to only consider 5’ end motifs on the negative strand.

-
Default: False

+
Default: False

 

 
-o, --output-file

 
TSV to print k-mer frequencies. If “-”, will write to stdout.

-
Default: '-'

+
Default: “-”

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 20

+
Default: 20

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -900,7 +903,8 @@ 
Named Arguments
 
interval-end-motifs#

 
Measures frequency of k-mer 5’ end motifs in each region specified in a BED file and writes data into a table.

-
finaletoolkit interval-end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-B] [-n] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
+
finaletoolkit interval-end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-B] [-n] [-o OUTPUT_FILE]
+                                  [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
                                   input_file refseq_file intervals
 

 

@@ -918,16 +922,16 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-k

 
Length of k-mer.

-
Default: 4

+
Default: 4

 

 
-min, --min-length

 
Minimum length for a fragment to be included.

-
Default: 0

+
Default: 0

 

 
-max, --max-length

 
Maximum length for a fragment to be included.

@@ -940,27 +944,27 @@ 
Named ArgumentsTrue

+
Default: True

 

 
-n, --negative-strand

 
Set flag in conjunction with -B to only consider 5’ end motifs on the negative strand.

-
Default: False

+
Default: False

 

 
-o, --output-file

 
Path to TSV or CSV file to write end motif frequencies to.

-
Default: '-'

+
Default: “-”

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 20

+
Default: 20

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -976,20 +980,20 @@ 
Positional Arguments
 
file_path

 
Tab-delimited or similar file containing one column for all k-mers a one column for frequency. Reads from stdin by default.

-
Default: '-'

+
Default: “-”

 

 

 

-

-
Named Arguments#

+

+
Named Arguments#

 

 
-s, --sep

 
Separator used in tabular file.

-
Default: '    '

+
Default: “      “

 

 
--header

 
Number of header rows to ignore. Default is 0

-
Default: 0

+
Default: 0

 

 

 

@@ -1005,24 +1009,24 @@ 
Positional Arguments
 
file_path

 
Tab-delimited or similar file containing one column for all k-mers a one column for frequency. Reads from stdin by default.

-
Default: '-'

+
Default: “-”

 

 
file_out

 
Path to the output BED/BEDGraph file containing MDS for each interval.

-
Default: '-'

+
Default: “-”

 

 

 

-

-
Named Arguments#

+

+
Named Arguments#

 

 
-s, --sep

 
Separator used in tabular file.

-
Default: '    '

+
Default: “      “

 

 
--header

 
Number of header rows to ignore. Default is 0

-
Default: 0

+
Default: 0

 

 

 

@@ -1030,8 +1034,8 @@ 
Named Arguments
 
filter-file#

 
Filters a BED/BAM/CRAM file so that all reads/intervals, when applicable,are in mapped pairs, exceed a certain MAPQ, are not flagged for quality, are read1, are not secondary or supplementary alignments, are within/excluding specified intervals, and are on the same reference sequence as the mate.

-
finaletoolkit filter-file [-h] [-W WHITELIST_FILE] [-B BLACKLIST_FILE] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-lo MIN_LENGTH]
-                          [-hi MAX_LENGTH] [-w WORKERS] [-v]
+
finaletoolkit filter-file [-h] [-W WHITELIST_FILE] [-B BLACKLIST_FILE] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-min MIN_LENGTH] [-max MAX_LENGTH]
+                          [-p {midpoint,any}] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-w WORKERS] [-v]
                           input_file
 

 

@@ -1043,8 +1047,8 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-W, --whitelist-file

 
Only output alignments overlapping the intervals in this BED file will be included.

@@ -1054,11 +1058,11 @@ 
Named Arguments
 
-o, --output-file

 
Output BED/BAM/CRAM file path.

-
Default: '-'

+
Default: “-”

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 30

+
Default: 30

 

 
-min, --min-length

 
Minimum length for a fragment to be included.

@@ -1069,7 +1073,7 @@ 
Named Arguments-p, --intersect-policy
 
Possible choices: midpoint, any

 
Specifies what policy is used to include/exclude fragments in the given interval. See User Guide for more information.

-
Default: 'midpoint'

+
Default: “midpoint”

 

 
-lo, --fraction-low

 
Deprecated alias for –min-length

@@ -1079,7 +1083,7 @@ 
Named Arguments
 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

@@ -1106,20 +1110,20 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-o, --output-file

 
A wiggle file containing the aggregate signal over the intervals specified in interval file.

-
Default: '-'

+
Default: “-”

 

 
-m, --median-window-size

 
Size of the median filter window used to aggregate scores. Set to 120 if aggregating WPS signals.

-
Default: 1

+
Default: 1

 

 
-a, --mean

 
use mean instead

-
Default: False

+
Default: False

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

@@ -1197,76 +1201,76 @@ 
Positional Arguments
     
    
-
  • Named Arguments
    • 
+
  • Named Arguments
    • 
 
  • Sub-commands
      
 
    • coverage
 
      • 
 
    • frag-length-bins
 
      • 
 
    • frag-length-intervals
 
      • 
 
    • cleavage-profile
 
      • 
 
    • wps
 
      • 
 
    • adjust-wps
 
      • 
 
    • delfi
 
      • 
 
    • delfi-gc-correct
 
      • 
 
    • end-motifs
 
      • 
 
    • interval-end-motifs
 
      • 
 
    • mds
 
      • 
 
    • interval-mds
 
      • 
 
    • filter-file
 
      • 
 
    • agg-bw
 
      • 
 
    • gap-bed
        
@@ -1321,7 +1325,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/index.html b/docs/_build/html/documentation/index.html
index fe0d28e1..16ba5e2d 100644
--- a/docs/_build/html/documentation/index.html
+++ b/docs/_build/html/documentation/index.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -461,7 +461,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/features.html b/docs/_build/html/documentation/user_guide/features.html
index 062646d5..9422c29b 100644
--- a/docs/_build/html/documentation/user_guide/features.html
+++ b/docs/_build/html/documentation/user_guide/features.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -496,7 +496,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/help.html b/docs/_build/html/documentation/user_guide/help.html
index 91320f0e..0d9e280d 100644
--- a/docs/_build/html/documentation/user_guide/help.html
+++ b/docs/_build/html/documentation/user_guide/help.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -453,7 +453,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/index.html b/docs/_build/html/documentation/user_guide/index.html
index fee66f99..e17958c1 100644
--- a/docs/_build/html/documentation/user_guide/index.html
+++ b/docs/_build/html/documentation/user_guide/index.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -481,7 +481,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/inputdata.html b/docs/_build/html/documentation/user_guide/inputdata.html
index 6d24acb0..c0dc6e56 100644
--- a/docs/_build/html/documentation/user_guide/inputdata.html
+++ b/docs/_build/html/documentation/user_guide/inputdata.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -509,7 +509,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/installation.html b/docs/_build/html/documentation/user_guide/installation.html
index 56f1329d..89c1478b 100644
--- a/docs/_build/html/documentation/user_guide/installation.html
+++ b/docs/_build/html/documentation/user_guide/installation.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -480,7 +480,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/intersectpolicy.html b/docs/_build/html/documentation/user_guide/intersectpolicy.html
index 6f8ae67c..a14d1208 100644
--- a/docs/_build/html/documentation/user_guide/intersectpolicy.html
+++ b/docs/_build/html/documentation/user_guide/intersectpolicy.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -470,7 +470,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/quickstart.html b/docs/_build/html/documentation/user_guide/quickstart.html
index 7fa4d99b..acedb411 100644
--- a/docs/_build/html/documentation/user_guide/quickstart.html
+++ b/docs/_build/html/documentation/user_guide/quickstart.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -380,12 +380,12 @@ 
        Importing Modules
        >>> import finaletoolkit.frag as ft
+
        >>> import finaletoolkit.frag as ft
 
        
 
        
 
        If you want to load a specific function, you can do so by using the following:
        
 
        Assuming we wanted to load the DELFI function:
        
-
        >>> from finaletoolkit.frag import delfi
+
        >>> from finaletoolkit.frag import delfi
 
        
 
        
 
        For more detailed tutorials, please check out our [wiki](epifluidlab/FinaleToolkit).
        
@@ -487,7 +487,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/structure.html b/docs/_build/html/documentation/user_guide/structure.html
index 541edc8e..2ba7b9a4 100644
--- a/docs/_build/html/documentation/user_guide/structure.html
+++ b/docs/_build/html/documentation/user_guide/structure.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -458,7 +458,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/what.html b/docs/_build/html/documentation/user_guide/what.html
index 2ade4db6..3a9b285f 100644
--- a/docs/_build/html/documentation/user_guide/what.html
+++ b/docs/_build/html/documentation/user_guide/what.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -449,7 +449,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html
index aabac183..164ba64b 100644
--- a/docs/_build/html/genindex.html
+++ b/docs/_build/html/genindex.html
@@ -29,7 +29,7 @@
   
 
 
-    
+    
   
   
   
@@ -38,7 +38,7 @@
 
 
     
-    
+    
     
     
     
@@ -607,7 +607,7 @@ 
        W
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
index 09809725..0ce0fda2 100644
--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
@@ -30,7 +30,7 @@
   
 
 
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@@ -375,7 +375,7 @@ 
        Citationsyear = {2024},
     doi = {10.1101/2024.05.29.596414},
     publisher = {Cold Spring Harbor Laboratory},
-    abstract = {Cell-free DNA (cfDNA) fragmentation pattern represents a promising non-invasive biomarker for disease diagnosis and prognosis. Numerous fragmentation features, such as end motif and window protection score (WPS), have been characterized in cfDNA genomic sequencing. However, the analytical tools developed in these studies are often not released to the liquid biopsy community or are inefficient for genome-wide analysis in large datasets. To address this gap, we have developed FinaleToolkit, a fast and memory efficient Python package designed to generate comprehensive fragmentation features from large cfDNA genomic sequencing data. For instance, FinaleToolkit can generate genome-wide WPS features from a \~{}100X cfDNA whole-genome sequencing (WGS) dataset in 1.2 hours using 16 CPU cores, offering up to a \~{}50-fold increase in processing speed compared to original implementations in the same dataset. We have benchmarked FinaleToolkit against original studies or implementations where possible, confirming its efficacy. Furthermore, FinaleToolkit enabled the genome-wide analysis of fragmentation patterns over arbitrary genomic intervals, significantly boosting the performance for cancer early detection. FinaleToolkit is open source and thoroughly documented with both command line interface and Python application programming interface (API) to facilitate its widespread adoption and use within the research community: https://github.com/epifluidlab/FinaleToolkitCompeting Interest StatementY.L. owns stocks from Freenome Inc. The remaining authors declare no competing interests.},
+    abstract = {Cell-free DNA (cfDNA) fragmentation pattern represents a promising non-invasive biomarker for disease diagnosis and prognosis. Numerous fragmentation features, such as end motif and window protection score (WPS), have been characterized in cfDNA genomic sequencing. However, the analytical tools developed in these studies are often not released to the liquid biopsy community or are inefficient for genome-wide analysis in large datasets. To address this gap, we have developed FinaleToolkit, a fast and memory efficient Python package designed to generate comprehensive fragmentation features from large cfDNA genomic sequencing data. For instance, FinaleToolkit can generate genome-wide WPS features from a \~{}100X cfDNA whole-genome sequencing (WGS) dataset in 1.2 hours using 16 CPU cores, offering up to a \~{}50-fold increase in processing speed compared to original implementations in the same dataset. We have benchmarked FinaleToolkit against original studies or implementations where possible, confirming its efficacy. Furthermore, FinaleToolkit enabled the genome-wide analysis of fragmentation patterns over arbitrary genomic intervals, significantly boosting the performance for cancer early detection. FinaleToolkit is open source and thoroughly documented with both command line interface and Python application programming interface (API) to facilitate its widespread adoption and use within the research community: https://github.com/epifluidlab/FinaleToolkitCompeting Interest StatementY.L. owns stocks from Freenome Inc. The remaining authors declare no competing interests.},
     URL = {https://www.biorxiv.org/content/early/2024/06/02/2024.05.29.596414},
     eprint = {https://www.biorxiv.org/content/early/2024/06/02/2024.05.29.596414.full.pdf},
     journal = {bioRxiv}
@@ -493,7 +493,7 @@ 
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diff --git a/docs/_build/html/search.html b/docs/_build/html/search.html
index 330ad2cb..efff236c 100644
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        Search
        
         
        
 
   
        
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diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js
index 3a29ebc1..5317efa7 100644
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