From 90d29ecf7de42c6d3d15db0d7eac5d2766f5cf37 Mon Sep 17 00:00:00 2001 From: Kundan Baliga Date: Wed, 8 Jan 2025 19:06:36 -0500 Subject: [PATCH] documentation update --- .../api_reference/basicfeatures.doctree | Bin 90956 -> 91247 bytes .../api_reference/cleavageprofile.doctree | Bin 30431 -> 32112 bytes .../documentation/api_reference/delfi.doctree | Bin 44920 -> 43586 bytes .../api_reference/endmotifs.doctree | Bin 182193 -> 183509 bytes .../api_reference/fragfile.doctree | Bin 104096 -> 140206 bytes .../api_reference/genomeutils.doctree | Bin 80099 -> 80902 bytes .../documentation/api_reference/index.doctree | Bin 3094 -> 3091 bytes .../documentation/api_reference/wps.doctree | Bin 98876 -> 101673 bytes .../documentation/cli_reference/index.doctree | Bin 244553 -> 256599 bytes .../doctrees/documentation/index.doctree | Bin 3138 -> 3135 bytes .../documentation/user_guide/features.doctree | Bin 11892 -> 11889 bytes .../documentation/user_guide/help.doctree | Bin 5456 -> 5453 bytes 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When it is not found, a full rebuild will be done. -config: 670efaa449e3fccfe64f8fb2cf4a7d46 +# This file records the configuration used when building these files. When it is not found, a full rebuild will be done. +config: a6a7c49fe85dc34358516258c905dd38 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/_build/html/.buildinfo.bak b/docs/_build/html/.buildinfo.bak new file mode 100644 index 00000000..b87a602b --- /dev/null +++ b/docs/_build/html/.buildinfo.bak @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# 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/_sources/documentation/api_reference/fragfile.rst.txt b/docs/_build/html/_sources/documentation/api_reference/fragfile.rst.txt index a4774294..546d2f30 100644 --- a/docs/_build/html/_sources/documentation/api_reference/fragfile.rst.txt +++ b/docs/_build/html/_sources/documentation/api_reference/fragfile.rst.txt @@ -1,7 +1,7 @@ Frag File Utilities ====================================== -.. autofunction:: finaletoolkit.utils.filter_bam +.. autofunction:: finaletoolkit.utils.filter_file .. autofunction:: finaletoolkit.utils.agg_bw diff --git a/docs/_build/html/_static/basic.css b/docs/_build/html/_static/basic.css index f316efcb..7ebbd6d0 100644 --- a/docs/_build/html/_static/basic.css +++ b/docs/_build/html/_static/basic.css @@ -1,12 +1,5 @@ /* - * basic.css - * ~~~~~~~~~ - * * Sphinx stylesheet -- basic theme. - * - * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS. - * :license: BSD, see LICENSE for details. - * */ /* -- main layout ----------------------------------------------------------- */ @@ -115,15 +108,11 @@ img { /* -- search page ----------------------------------------------------------- */ ul.search { - margin: 10px 0 0 20px; - padding: 0; + margin-top: 10px; } ul.search li { - padding: 5px 0 5px 20px; - background-image: url(file.png); - background-repeat: no-repeat; - background-position: 0 7px; + padding: 5px 0; } ul.search li a { diff --git a/docs/_build/html/_static/doctools.js b/docs/_build/html/_static/doctools.js index 4d67807d..0398ebb9 100644 --- a/docs/_build/html/_static/doctools.js +++ b/docs/_build/html/_static/doctools.js @@ -1,12 +1,5 @@ /* - * 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 367b8ed8..c7fe6c6f 100644 --- a/docs/_build/html/_static/language_data.js +++ b/docs/_build/html/_static/language_data.js @@ -1,13 +1,6 @@ /* - * 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 012e6a00..d7dd5778 100644 --- a/docs/_build/html/_static/pygments.css +++ 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+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 b08d58c9..2c774d17 100644 --- a/docs/_build/html/_static/searchtools.js +++ b/docs/_build/html/_static/searchtools.js @@ -1,12 +1,5 @@ /* - * 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"; @@ -20,7 +13,7 @@ if (typeof Scorer === "undefined") { // and returns the new score. /* score: result => { - const [docname, title, anchor, descr, score, filename] = result + const [docname, title, anchor, descr, score, filename, kind] = result return score }, */ @@ -47,6 +40,14 @@ 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); }; @@ -64,9 +65,13 @@ 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] = item; + const [docName, title, anchor, descr, score, _filename, kind] = 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") { @@ -115,8 +120,10 @@ 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 = _( - "Search finished, found ${resultCount} page(s) matching the search query." + Search.status.innerText = Documentation.ngettext( + "Search finished, found one page matching the search query.", + "Search finished, found ${resultCount} pages matching the search query.", + resultCount, ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( @@ -138,7 +145,7 @@ 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]. +// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. // 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) => { @@ -248,6 +255,7 @@ 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"); @@ -318,7 +326,7 @@ 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]. + // Each is an array of [docname, title, anchor, descr, score, filename, kind]. const normalResults = []; const nonMainIndexResults = []; @@ -337,6 +345,7 @@ const Search = { null, score + boost, filenames[file], + SearchResultKind.title, ]); } } @@ -354,6 +363,7 @@ const Search = { null, score, filenames[file], + SearchResultKind.index, ]; if (isMain) { normalResults.push(result); @@ -475,6 +485,7 @@ const Search = { descr, score, filenames[match[0]], + SearchResultKind.object, ]); }; Object.keys(objects).forEach((prefix) => @@ -585,6 +596,7 @@ 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 2ed2238d..9c168def 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 | 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]]#
+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]]#

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 | 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#
+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#

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 | 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]#
+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]#

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 7.4.7. + Created using Sphinx 8.1.3.

diff --git a/docs/_build/html/documentation/api_reference/cleavageprofile.html b/docs/_build/html/documentation/api_reference/cleavageprofile.html index f66959e4..0a1941ab 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: 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#
+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#

Cleavage profile calculated over a single interval.

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

This Page

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

diff --git a/docs/_build/html/documentation/api_reference/delfi.html b/docs/_build/html/documentation/api_reference/delfi.html index 827323ff..3a70b718 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 = 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#
+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#

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

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

This Page

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

diff --git a/docs/_build/html/documentation/api_reference/endmotifs.html b/docs/_build/html/documentation/api_reference/endmotifs.html index 43b6d80b..4ffc3b42 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 7.4.7. + Created using Sphinx 8.1.3.

diff --git a/docs/_build/html/documentation/api_reference/fragfile.html b/docs/_build/html/documentation/api_reference/fragfile.html index ddaa7c97..5258675b 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 @@ - + @@ -360,6 +360,43 @@

Frag File Utilities#

+
+
+finaletoolkit.utils.filter_file(input_file: str, whitelist_file: str | None = None, blacklist_file: str | None = None, output_file: str | None = None, min_length: int | None = None, max_length: int | None = None, intersect_policy: str = 'midpoint', quality_threshold: int = 30, workers: int = 1, verbose: bool = False, fraction_low: int | None = None, fraction_high: int | None = None)#
+

Accepts the path to a BAM, CRAM, or BED file and creates a filtered version.

+

Filter reads/intervals based on exceeding the specified quality threshold, +intersections with a region in the region bed (if provided), and read length.

+

For BAM/CRAM files, it also filters reads based on being read1 in a proper pair.

+
+
Parameters:
+
    +

  • input_file (str) – Path string to the input BAM, CRAM, or BED file.

    • +

  • whitelist_file (str, optional) – Path to a BED file defining regions to include.

    • +

  • blacklist_file (str, optional) – Path to a BED file defining regions to exclude.

    • +

  • output_file (str, optional) – Path to the output filtered file. If None, a temporary file is created.

    • +

  • min_length (int, optional) – Minimum length for reads/intervals

    • +

  • max_length (int, optional) – Maximum length for reads/intervals

    • +

  • intersect_policy (str, optional) – Specifies how to determine whether fragments are in interval for +whitelisting and blacklisting functionality.’midpoint’ (default) +calculates the central coordinate of each fragment and only +selects the fragment if the midpoint is in the interval. +‘any’ includes fragments with any overlap with the interval.

    • +

  • quality_threshold (int, optional) – Minimum mapping quality score

    • +

  • workers (int, optional) – Number of worker threads for samtools.

    • +

  • verbose (bool, optional) – Default is False

    • +

  • fraction_low (int, optional) – Deprecated alias for min_length

    • +

  • fraction_high (int, optional) – Deprecated alias for max_length

    • +
+
+
Returns:
+

output_file – Path to the filtered output file.

+
+
Return type:
+

str

+
+
+
+
finaletoolkit.utils.agg_bw(input_file: str | PathLike, interval_file: str | PathLike, output_file: str | PathLike, median_window_size: int = 1, mean: bool = False, verbose: bool = False)#
@@ -474,7 +511,7 @@

Frag File Utilities
-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#
+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]]#

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

@@ -593,6 +630,7 @@

Frag File Utilities
    +
  • filter_file()
  • agg_bw()
  • chrom_sizes_to_list()
  • chrom_sizes_to_dict()
    • @@ -646,7 +684,7 @@

    This Page

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

    diff --git a/docs/_build/html/documentation/api_reference/genomeutils.html b/docs/_build/html/documentation/api_reference/genomeutils.html index 72179329..86dd663d 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 7.4.7. + Created using Sphinx 8.1.3.

    diff --git a/docs/_build/html/documentation/api_reference/index.html b/docs/_build/html/documentation/api_reference/index.html index 9180ec60..e40dee31 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 @@ - + @@ -390,6 +390,7 @@

    API#

  • Frag File Utilities
      +
    • filter_file()
    • agg_bw()
    • chrom_sizes_to_list()
    • chrom_sizes_to_dict()
      • @@ -493,7 +494,7 @@

      This Page

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

      diff --git a/docs/_build/html/documentation/api_reference/wps.html b/docs/_build/html/documentation/api_reference/wps.html index abe1de2d..b3476e11 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 | 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#
      +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#

      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: 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)#
      +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)#

      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 7.4.7. + Created using Sphinx 8.1.3.

      diff --git a/docs/_build/html/documentation/cli_reference/index.html b/docs/_build/html/documentation/cli_reference/index.html index 1b562c55..bc4df73f 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

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

      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
 
      
 
      
@@ -384,24 +383,24 @@ 
      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.

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

      Named Arguments'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

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

      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
 
      
 
      
@@ -442,8 +441,8 @@ 
      Positional Arguments
-
      Named Arguments#
      
+
      
+
      Named Arguments#
      
 
      
 
      -c, --contig
      
 
      Specify the contig or chromosome to select fragments from. (Required if using –start or –stop.)
      
@@ -456,7 +455,7 @@ 
      Named Arguments0
      
 
      
 
      -max, --max-length
      
 
      Maximum length for a fragment to be included in fragment length.
      
@@ -464,26 +463,26 @@ 
      Named Arguments'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
      
 
      
 
      
 
      
@@ -491,8 +490,7 @@ 
      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
 
      
 
      
 
      
@@ -506,12 +504,12 @@ 
      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.
      
@@ -519,23 +517,23 @@ 
      Named Arguments'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
      
 
      
 
      
 
      
@@ -543,8 +541,8 @@ 
      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
 
      
 
      
@@ -559,19 +557,19 @@ 
      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.
      
@@ -584,23 +582,23 @@ 
      Named Arguments20
      
 
      
 
      -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
      
 
      
 
      
 
      
@@ -608,8 +606,8 @@ 
      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
 
      
 
      
@@ -624,31 +622,31 @@ 
      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.
      
@@ -658,15 +656,15 @@ 
      Named Arguments30
      
 
      
 
      -w, --workers
      
 
      Number of worker processes.
      
-
      Default: 1
      
+
      Default: 1
      
 
      
 
      -v, --verbose
      
 
      Enable verbose mode to display detailed processing information.
      
-
      Default: 0
      
+
      Default: 0
      
 
      
 
      
 
      
@@ -674,8 +672,8 @@ 
      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
 
      
 
      
@@ -693,48 +691,48 @@ 
      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.
      
@@ -766,8 +764,8 @@ 
      Positional Arguments
-
      Named Arguments#
      
+
      
+
      Named Arguments#
      
 
      
 
      -b, --blacklist-file
      
 
      BED file containing regions to ignore when calculating DELFI.
      
@@ -777,35 +775,35 @@ 
      Named Arguments'-'
      
 
      
 
      -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
      
 
      
 
      
 
      
@@ -824,16 +822,16 @@ 
      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.
      
@@ -844,8 +842,7 @@ 
      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
 
      
 
      
 
      
@@ -859,43 +856,43 @@ 
      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
      
 
      
 
      
 
      
@@ -903,8 +900,7 @@ 
      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
 
      
 
      
@@ -922,16 +918,16 @@ 
      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.
      
@@ -944,27 +940,27 @@ 
      Named Arguments
 
      -B, --single-strand
      
 
      Set flag to only consider one strand for end-motifs. By default, the positive strand is calculated, but with the -n flag, the 5’ end motifs of the negative strand are considered instead.
      
-
      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
      
 
      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
      
 
      
 
      
 
      
@@ -980,20 +976,20 @@ 
      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
      
 
      
 
      
 
      
@@ -1009,24 +1005,24 @@ 
      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
      
 
      
 
      
 
      
@@ -1034,8 +1030,8 @@ 
      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]
-                          [-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
 
      
 
      
@@ -1047,8 +1043,8 @@ 
      Positional Arguments
-
      Named Arguments#
      
+
      
+
      Named Arguments#
      
 
      
 
      -W, --whitelist-file
      
 
      Only output alignments overlapping the intervals in this BED file will be included.
      
@@ -1058,11 +1054,11 @@ 
      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.
      
@@ -1070,6 +1066,11 @@ 
      Named Arguments-max, --max-length
 
      Maximum length for a fragment to be included.
      
 
      
+
      -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'
      
+
      
 
      -lo, --fraction-low
      
 
      Deprecated alias for –min-length
      
 
      
@@ -1078,7 +1079,7 @@ 
      Named Arguments
 
      -w, --workers
      
 
      Number of worker processes.
      
-
      Default: 1
      
+
      Default: 1
      
 
      
 
      -v, --verbose
      
 
      Enable verbose mode to display detailed processing information.
      
@@ -1105,20 +1106,20 @@ 
      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.
      
@@ -1196,76 +1197,76 @@ 
      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
            
@@ -1320,7 +1321,7 @@ 
            This Page
            
         
            
 
   
            
-    Created using Sphinx 7.4.7.
+    Created using Sphinx 8.1.3.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/index.html b/docs/_build/html/documentation/index.html
index 16ba5e2d..fe0d28e1 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 7.4.7.
+    Created using Sphinx 8.1.3.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/user_guide/features.html b/docs/_build/html/documentation/user_guide/features.html
index 9422c29b..062646d5 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 7.4.7.
+    Created using Sphinx 8.1.3.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/user_guide/help.html b/docs/_build/html/documentation/user_guide/help.html
index 0d9e280d..91320f0e 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 7.4.7.
+    Created using Sphinx 8.1.3.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/user_guide/index.html b/docs/_build/html/documentation/user_guide/index.html
index e17958c1..fee66f99 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 7.4.7.
+    Created using Sphinx 8.1.3.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/user_guide/inputdata.html b/docs/_build/html/documentation/user_guide/inputdata.html
index c0dc6e56..6d24acb0 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 7.4.7.
+    Created using Sphinx 8.1.3.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/user_guide/installation.html b/docs/_build/html/documentation/user_guide/installation.html
index 89c1478b..56f1329d 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 7.4.7.
+    Created using Sphinx 8.1.3.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/user_guide/intersectpolicy.html b/docs/_build/html/documentation/user_guide/intersectpolicy.html
index a14d1208..6f8ae67c 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 7.4.7.
+    Created using Sphinx 8.1.3.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/user_guide/quickstart.html b/docs/_build/html/documentation/user_guide/quickstart.html
index acedb411..7fa4d99b 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 7.4.7.
+    Created using Sphinx 8.1.3.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/user_guide/structure.html b/docs/_build/html/documentation/user_guide/structure.html
index 2ba7b9a4..541edc8e 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 7.4.7.
+    Created using Sphinx 8.1.3.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/user_guide/what.html b/docs/_build/html/documentation/user_guide/what.html
index 3a9b285f..2ade4db6 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 7.4.7.
+    Created using Sphinx 8.1.3.
     
            
   
            
 
            
diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html
index 67f8efb3..aabac183 100644
--- a/docs/_build/html/genindex.html
+++ b/docs/_build/html/genindex.html
@@ -29,7 +29,7 @@
   
 
 
-    
+    
   
   
   
@@ -38,7 +38,7 @@
 
 
     
-    
+    
     
     
     
@@ -400,6 +400,8 @@ 
            E
            
 
            F
            
 
            
   
              
+      
            • filter_file() (in module finaletoolkit.utils)
+
              • 
       
            • frag_array() (in module finaletoolkit.utils)
 
              • 
       
            • frag_generator() (in module finaletoolkit.utils)
@@ -605,7 +607,7 @@ 
              W
              
         
              
 
   
              
-    Created using Sphinx 7.4.7.
+    Created using Sphinx 8.1.3.
     
              
   
              
 
              
diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
index 0d1b851e..3f133547 100644
--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -348,7 +348,7 @@ 
              DocumentationCLI
 
              • 
@@ -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 @@ 
              This Page
              
         
              
 
   
              
-    Created using Sphinx 7.4.7.
+    Created using Sphinx 8.1.3.
     
              
   
              
 
              
diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv
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