From 672872b792d515fca02bf946ac78a11fcf804163 Mon Sep 17 00:00:00 2001 From: Marcus Sherman Date: Tue, 2 Apr 2019 12:12:16 -0400 Subject: [PATCH] fixed FileNotFoundError `version` file was accidentally left out of `setup.py` file. This has been included now. --- MANIFEST.in | 1 + codemeta.json | 4 +- docs/build/doctrees/bamnostic.doctree | Bin 374530 -> 374501 bytes docs/build/doctrees/environment.pickle | Bin 147873 -> 147745 bytes docs/build/doctrees/index.doctree | Bin 5674 -> 5704 bytes docs/build/doctrees/install.doctree | Bin 7719 -> 6307 bytes docs/build/doctrees/quickstart.doctree | Bin 127664 -> 23494 bytes docs/build/html/.buildinfo | 2 +- docs/build/html/_modules/bamnostic/bai.html | 4 +- docs/build/html/_modules/bamnostic/bgzf.html | 4 +- docs/build/html/_modules/bamnostic/core.html | 4 +- docs/build/html/_modules/bamnostic/utils.html | 4 +- docs/build/html/_modules/index.html | 4 +- docs/build/html/_static/basic.css | 74 +- docs/build/html/_static/doctools.js | 5 +- .../html/_static/documentation_options.js | 4 +- docs/build/html/_static/searchtools.js | 54 +- docs/build/html/bamnostic.html | 1099 ++++++++--------- docs/build/html/genindex.html | 4 +- docs/build/html/index.html | 14 +- docs/build/html/install.html | 28 +- docs/build/html/objects.inv | Bin 1154 -> 1155 bytes docs/build/html/py-modindex.html | 18 +- docs/build/html/quickstart.html | 56 +- docs/build/html/search.html | 4 +- docs/build/html/searchindex.js | 2 +- docs/build/html/support.html | 7 +- docs/paper/codemeta.json | 4 +- setup.py | 2 +- version | 2 +- 30 files changed, 689 insertions(+), 715 deletions(-) diff --git a/MANIFEST.in b/MANIFEST.in index 555426d..7baa7c2 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -5,3 +5,4 @@ include ./docs/build/* include ./CONTRIBUTING* include ./CODE_OF_CONDUCT* include ./requirements.txt +include ./version diff --git a/codemeta.json b/codemeta.json index ef80a6d..f693555 100644 --- a/codemeta.json +++ b/codemeta.json @@ -37,8 +37,8 @@ "description": "BAMnostic is a Pure Python OS, version, and runtime agnostic BAM file parser", "keywords": "BAM, pysam, genomics, genetics, htslib, samtools", "license": 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z3o0rAr)6t>K`$=U^aTSno`LIxQCzl8uNdi4C6me+Wv~x`$x%&rrAx(mpa~kuWm4se zF`qlOob9qU=ryyHa&N(2=U`OpGquHXiW?p%mfj%!gO#FQAW658-U00vt0ei|Tji=z z%al^b7KurnY8)$kKMQt_a5;66RpH zL`NAgEI|?OY;ips=p&U!yT7&Fcg)dL1*Y;(q zP)h5L2G31rb;v1@zIL{P6eHzN3cfy4D}yi_pzJYoCaA~G?r#GlDW!A8c}QxO|2L5m zp<0_0-#gV_Uxnh&+9cd9>Wjb{ZbNMI{Gy9k ze}>*)O>WxZo_rGWXMQ#Lbv8Ml@+|V}RSEdDpZxj?9L|`3g8cgRb?|G6{QBqy`1KI^ z^)DB~uYV%HF6o9}yUDLFp8>xfC%?XYE(wueThE7I8u@j%2EUfcuNTN?KPSHuaNtq? zS8yn2K0(Cz6{&))wM0hqc$qS>rJSV_&Qj@SsbsTMs#z-0ER|-KN-|5OfZqTsehbkf>Q6< z3?WK=FVO_0{#Bw0O8u)u6O{TzL=%+yy&8llb#fLcrJg4>f6ZF&%_20_)~9n&1CV5g zl(g@VVvN0Kn}_#~{T>(%WR%6ZQi10>`s!xiP5$;;A;z@~m438Ih~M@WASZVF<8q#? uverN$%U|12)+ - bamnostic.bai — bamnostic 1.0.9 documentation + bamnostic.bai — bamnostic 1.0.10 documentation @@ -59,7 +59,7 @@

- 1.0.9 + 1.0.10
diff --git a/docs/build/html/_modules/bamnostic/bgzf.html b/docs/build/html/_modules/bamnostic/bgzf.html index c6eeba7..05e7177 100644 --- a/docs/build/html/_modules/bamnostic/bgzf.html +++ b/docs/build/html/_modules/bamnostic/bgzf.html @@ -8,7 +8,7 @@ - bamnostic.bgzf — bamnostic 1.0.9 documentation + bamnostic.bgzf — bamnostic 1.0.10 documentation @@ -59,7 +59,7 @@
- 1.0.9 + 1.0.10
diff --git a/docs/build/html/_modules/bamnostic/core.html b/docs/build/html/_modules/bamnostic/core.html index 7bec949..2685ea1 100644 --- a/docs/build/html/_modules/bamnostic/core.html +++ b/docs/build/html/_modules/bamnostic/core.html @@ -8,7 +8,7 @@ - bamnostic.core — bamnostic 1.0.9 documentation + bamnostic.core — bamnostic 1.0.10 documentation @@ -59,7 +59,7 @@
- 1.0.9 + 1.0.10
diff --git a/docs/build/html/_modules/bamnostic/utils.html b/docs/build/html/_modules/bamnostic/utils.html index 4cfcbfc..6891686 100644 --- a/docs/build/html/_modules/bamnostic/utils.html +++ b/docs/build/html/_modules/bamnostic/utils.html @@ -8,7 +8,7 @@ - bamnostic.utils — bamnostic 1.0.9 documentation + bamnostic.utils — bamnostic 1.0.10 documentation @@ -59,7 +59,7 @@
- 1.0.9 + 1.0.10
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html index 57be0c7..c8d7fb8 100644 --- a/docs/build/html/_modules/index.html +++ b/docs/build/html/_modules/index.html @@ -8,7 +8,7 @@ - Overview: module code — bamnostic 1.0.9 documentation + Overview: module code — bamnostic 1.0.10 documentation @@ -59,7 +59,7 @@
- 1.0.9 + 1.0.10
diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css index 0807176..53acd09 100644 --- a/docs/build/html/_static/basic.css +++ b/docs/build/html/_static/basic.css @@ -231,6 +231,16 @@ a.headerlink { visibility: hidden; } +a.brackets:before, +span.brackets > a:before{ + content: "["; +} + +a.brackets:after, +span.brackets > a:after { + content: "]"; +} + h1:hover > a.headerlink, h2:hover > a.headerlink, h3:hover > a.headerlink, @@ -391,6 +401,16 @@ table.citation td { border-bottom: none; } +th > p:first-child, +td > p:first-child { + margin-top: 0px; +} + +th > p:last-child, +td > p:last-child { + margin-bottom: 0px; +} + /* -- figures --------------------------------------------------------------- */ div.figure { @@ -460,11 +480,57 @@ ol.upperroman { list-style: upper-roman; } +li > p:first-child { + margin-top: 0px; +} + +li > p:last-child { + margin-bottom: 0px; +} + +dl.footnote > dt, +dl.citation > dt { + float: left; +} + +dl.footnote > dd, +dl.citation > dd { + margin-bottom: 0em; +} + +dl.footnote > dd:after, +dl.citation > dd:after { + content: ""; + clear: both; +} + +dl.field-list { + display: flex; + flex-wrap: wrap; +} + +dl.field-list > dt { + flex-basis: 20%; + font-weight: bold; + word-break: break-word; +} + +dl.field-list > dt:after { + content: ":"; +} + +dl.field-list > dd { + flex-basis: 70%; + padding-left: 1em; + margin-left: 0em; + margin-bottom: 0em; +} + dl { margin-bottom: 15px; } -dd p { +dd > p:first-child { margin-top: 0px; } @@ -537,6 +603,12 @@ dl.glossary dt { font-style: oblique; } +.classifier:before { + font-style: normal; + margin: 0.5em; + content: ":"; +} + abbr, acronym { border-bottom: dotted 1px; cursor: help; diff --git a/docs/build/html/_static/doctools.js b/docs/build/html/_static/doctools.js index 344db17..b33f87f 100644 --- a/docs/build/html/_static/doctools.js +++ b/docs/build/html/_static/doctools.js @@ -87,14 +87,13 @@ jQuery.fn.highlightText = function(text, className) { node.nextSibling)); node.nodeValue = val.substr(0, pos); if (isInSVG) { - var bbox = span.getBBox(); var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - rect.x.baseVal.value = bbox.x; + var bbox = node.parentElement.getBBox(); + rect.x.baseVal.value = bbox.x; rect.y.baseVal.value = bbox.y; rect.width.baseVal.value = bbox.width; rect.height.baseVal.value = bbox.height; rect.setAttribute('class', className); - var parentOfText = node.parentNode.parentNode; addItems.push({ "parent": node.parentNode, "target": rect}); diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js index f647e29..a07c9f2 100644 --- a/docs/build/html/_static/documentation_options.js +++ b/docs/build/html/_static/documentation_options.js @@ -1,10 +1,10 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '1.0.9', + VERSION: '1.0.10', LANGUAGE: 'en', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', HAS_SOURCE: true, SOURCELINK_SUFFIX: '.txt', - NAVIGATION_WITH_KEYS: false, + NAVIGATION_WITH_KEYS: false }; \ No newline at end of file diff --git a/docs/build/html/_static/searchtools.js b/docs/build/html/_static/searchtools.js index 5ff3180..4c58264 100644 --- a/docs/build/html/_static/searchtools.js +++ b/docs/build/html/_static/searchtools.js @@ -36,8 +36,10 @@ if (!Scorer) { // query found in title title: 15, + partialTitle: 7, // query found in terms - term: 5 + term: 5, + partialTerm: 2 }; } @@ -56,6 +58,14 @@ var Search = { _queued_query : null, _pulse_status : -1, + htmlToText : function(htmlString) { + var htmlElement = document.createElement('span'); + htmlElement.innerHTML = htmlString; + $(htmlElement).find('.headerlink').remove(); + docContent = $(htmlElement).find('[role=main]')[0]; + return docContent.textContent || docContent.innerText; + }, + init : function() { var params = $.getQueryParameters(); if (params.q) { @@ -65,16 +75,6 @@ var Search = { } }, - loadIndex : function(url) { - $.ajax({type: "GET", url: url, data: null, - dataType: "script", cache: true, - complete: function(jqxhr, textstatus) { - if (textstatus != "success") { - document.getElementById("searchindexloader").src = url; - } - }}); - }, - setIndex : function(index) { var q; this._index = index; @@ -120,7 +120,7 @@ var Search = { this.out = $('#search-results'); this.title = $('

' + _('Searching') + '

').appendTo(this.out); this.dots = $('').appendTo(this.title); - this.status = $('

').appendTo(this.out); + this.status = $('

 

').appendTo(this.out); this.output = $('
    ').appendTo(this.out); $('#search-progress').text(_('Preparing search...')); @@ -259,11 +259,7 @@ var Search = { displayNextItem(); }); } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) { - var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX; - if (suffix === undefined) { - suffix = '.txt'; - } - $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix), + $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX, dataType: "text", complete: function(jqxhr, textstatus) { var data = jqxhr.responseText; @@ -385,6 +381,19 @@ var Search = { {files: terms[word], score: Scorer.term}, {files: titleterms[word], score: Scorer.title} ]; + // add support for partial matches + if (word.length > 2) { + for (var w in terms) { + if (w.match(word) && !terms[word]) { + _o.push({files: terms[w], score: Scorer.partialTerm}) + } + } + for (var w in titleterms) { + if (w.match(word) && !titleterms[word]) { + _o.push({files: titleterms[w], score: Scorer.partialTitle}) + } + } + } // no match but word was a required one if ($u.every(_o, function(o){return o.files === undefined;})) { @@ -424,8 +433,12 @@ var Search = { var valid = true; // check if all requirements are matched - if (fileMap[file].length != searchterms.length) - continue; + var filteredTermCount = // as search terms with length < 3 are discarded: ignore + searchterms.filter(function(term){return term.length > 2}).length + if ( + fileMap[file].length != searchterms.length && + fileMap[file].length != filteredTermCount + ) continue; // ensure that none of the excluded terms is in the search result for (i = 0; i < excluded.length; i++) { @@ -456,7 +469,8 @@ var Search = { * words. the first one is used to find the occurrence, the * latter for highlighting it. */ - makeSearchSummary : function(text, keywords, hlwords) { + makeSearchSummary : function(htmlText, keywords, hlwords) { + var text = Search.htmlToText(htmlText); var textLower = text.toLowerCase(); var start = 0; $.each(keywords, function() { diff --git a/docs/build/html/bamnostic.html b/docs/build/html/bamnostic.html index 8a888ed..48871ea 100644 --- a/docs/build/html/bamnostic.html +++ b/docs/build/html/bamnostic.html @@ -8,7 +8,7 @@ - bamnostic package — bamnostic 1.0.9 documentation + bamnostic package — bamnostic 1.0.10 documentation @@ -61,7 +61,7 @@
    - 1.0.9 + 1.0.10
    @@ -171,18 +171,18 @@ outside of the standard library. Therefore, bamnostic will run on all stable versions of     PyPy.

    -

    Note

    -

    SAM and CRAM support is not yet implemented

    +

    Note

    +

    SAM and CRAM support is not yet implemented

    The three main classes of bamnostic are:

      -
    1. bamnostic.AlignmentFile: the BAM file handler
      2. -
    2. bamnostic.AlignedSegment: an aligned read object interface
      3. -
    3. bamnostic.bai.Bai: if the BAM file has an associated index file (preferred), this is the file handler for it.
      4. +

    4. bamnostic.AlignmentFile: the BAM file handler

      5. +

    5. bamnostic.AlignedSegment: an aligned read object interface

      6. +

    6. bamnostic.bai.Bai: if the BAM file has an associated index file (preferred), this is the file handler for it.

    -

    Note

    -

    Within the scope of personal research, reading BAM files is the only fully +

    Note

    +

    Within the scope of personal research, reading BAM files is the only fully supported IO. The skeleton for writing BAM files is present, just not connected.

    This code is part of the bamnostic distribution and governed by its @@ -195,20 +195,16 @@ class bamnostic.core.Cigar(op_code, n_op, op_id, op_name)

    Bases: tuple

    namedtuple for handling CIGAR data

    - --- - - - -
    Parameters:
      -
    • op_code (int) – CIGAR operation index
      • -
    • n_op (int) – number of operations for a given op_code
      • -
    • op_id (str) – the string representation of the CIGAR representation (‘MIDNSHP=XB’)
      • -
    • op_name (str) – Longer string name for operation
      • +
      +
      Parameters
      +
        +

      • op_code (int) – CIGAR operation index

        • +

      • n_op (int) – number of operations for a given op_code

        • +

      • op_id (str) – the string representation of the CIGAR representation (‘MIDNSHP=XB’)

        • +

      • op_name (str) – Longer string name for operation

      -
    +
    +
    n_op
    @@ -244,18 +240,17 @@ is the base-calling error probability. Phred quality scores tend range from 10 to 60. These qualities are then offset by 33 and ASCII-encoded for readability and storage.

    - --- - - - - - - - -
    Parameters:qual_string (str or bytes) – Phred quality scores without offset
    Returns:ASCII-encoded Phred scores offest by adding 33 to base score.
    Return type:(str)
    +
    +
    Parameters
    +

    qual_string (str or bytes) – Phred quality scores without offset

    +
    +
    Returns
    +

    ASCII-encoded Phred scores offest by adding 33 to base score.

    +
    +
    Return type
    +

    (str)

    +
    +

    Examples

    >>> qual_score = ''
 >>> ''.join(offset_qual(qual_score))
@@ -269,28 +264,24 @@
 class bamnostic.core.AlignmentFile(filepath_or_object, mode='rb', max_cache=128, index_filename=None, filename=None, check_header=False, check_sq=True, reference_filename=None, filepath_index=None, require_index=False, duplicate_filehandle=None, ignore_truncation=False, compresslevel=6, ignore_overwrite=False, copy_header=None, header=b'', reference_names=None, reference_lengths=None)[source]
 
    Bases: bamnostic.bam.BamReader, bamnostic.bam.BamWriter
    
 
    Wrapper to allow drop in replacement for BAM functionality in a pysam-like API.
    
-
---
-
-
-
-
    


    Parameters:
      
-
    • filepath_or_object (str | file) – the path or file object of the BAM file
      • 
-
    • mode (str) – Mode for reading. BAM files are binary by nature (default: ‘rb’).
      • 
-
    • max_cache (int) – number of desired LRU cache size, preferably a multiple of 2 (default: 128).
      • 
-
    • index_filename (str) – path to index file (BAI) if it is named differently than the BAM file (default: None).
      • 
-
    • filename (str | file) – synonym for filepath_or_object
      • 
-
    • check_header (bool) – Obsolete method maintained for backwards compatibility (default: False)
      • 
-
    • check_sq (bool) – Inspect BAM file for @SQ entries within the header
      • 
-
    • reference_filename (str) – Not implemented. Maintained for backwards compatibility
      • 
-
    • filepath_index (str) – synonym for index_filename
      • 
-
    • require_index (bool) – require the presence of an index file or raise (default: False)
      • 
-
    • duplicate_filehandle (bool) – Not implemented. Raises warning if True.
      • 
-
    • ignore_truncation (bool) – Whether or not to allow trucated file processing (default: False).
      • 
+
      
+
      Parameters
      
+
        
+
      • filepath_or_object (str | file) – the path or file object of the BAM file
        • 
+
      • mode (str) – Mode for reading. BAM files are binary by nature (default: ‘rb’).
        • 
+
      • max_cache (int) – number of desired LRU cache size, preferably a multiple of 2 (default: 128).
        • 
+
      • index_filename (str) – path to index file (BAI) if it is named differently than the BAM file (default: None).
        • 
+
      • filename (str | file) – synonym for filepath_or_object
        • 
+
      • check_header (bool) – Obsolete method maintained for backwards compatibility (default: False)
        • 
+
      • check_sq (bool) – Inspect BAM file for @SQ entries within the header
        • 
+
      • reference_filename (str) – Not implemented. Maintained for backwards compatibility
        • 
+
      • filepath_index (str) – synonym for index_filename
        • 
+
      • require_index (bool) – require the presence of an index file or raise (default: False)
        • 
+
      • duplicate_filehandle (bool) – Not implemented. Raises warning if True.
        • 
+
      • ignore_truncation (bool) – Whether or not to allow trucated file processing (default: False).
        • 
 
      
-
    
+
    
+
    @@ -479,40 +470,35 @@
    get_tag(tag, with_value_type=False)[source]

    Gets the value associated with a given tag key.

    - --- - - - - - -
    Parameters:
      -
    • tag (str) – the tag of interest
      • -
    • with_value_type (bool) – return what kind of value the tag
      • +
      +
      Parameters
      +
        +

      • tag (str) – the tag of interest

        • +

      • with_value_type (bool) – return what kind of value the tag

      -
    Returns:

    the value associated with a given tag or the value and type + +

    Returns
    +

    the value associated with a given tag or the value and type of value (as seen in BAM format)

    -
    +
    +
    get_tags(with_value_type=False)[source]

    Returns all the tags for a given read

    - --- - - - - - - - -
    Parameters:with_value_type (bool) – return the tag value type (as defined by BAM format)
    Returns:list of tag tuples (with or without tag value type)
    Return type:f_tags(list)
    +
    +
    Parameters
    +

    with_value_type (bool) – return the tag value type (as defined by BAM format)

    +
    +
    Returns
    +

    list of tag tuples (with or without tag value type)

    +
    +
    Return type
    +

    f_tags(list)

    +
    +
    @@ -520,17 +506,15 @@ get_cigar_stats()[source]

    Gets the counts of each CIGAR operation in the read and number of nucleotides related to those given operations.

    - --- - - - - - -
    Returns:list of CIGAR operation counts -nt_counts (list): list of nucleotide counts for each operation
    Return type:op_blocks (list)
    +
    +
    Returns
    +

    list of CIGAR operation counts +nt_counts (list): list of nucleotide counts for each operation

    +
    +
    Return type
    +

    op_blocks (list)

    +
    +
    @@ -540,32 +524,28 @@

    Uses the CIGAR string and MD tag to recreate the reference sequence associated with the aligned segment. This is done without the need for looking up the reference genome.

    - --- - - - - - - - -
    Returns:generated reference sequence
    Return type:(str)
    Raises:KeyError – if read does not contain MD tag
    +
    +
    Returns
    +

    generated reference sequence

    +
    +
    Return type
    +

    (str)

    +
    +
    Raises
    +

    KeyError – if read does not contain MD tag

    +
    +
    to_bam()[source]

    Writes the alignment record to a BAM file

    - --- - - - -
    Parameters:bam_file (string or bamnostic.bam.BamWriter) – BAM file path or open bam file in a write mode
    +
    +
    Parameters
    +

    bam_file (string or bamnostic.bam.BamWriter) – BAM file path or open bam file in a write mode

    +
    +
    @@ -635,27 +615,23 @@ it can be used to copy any BGZF block within a BAM file that starts at the given offset.

    -

    Note

    -

    Does not progress file cursor position.

    +

    Note

    +

    Does not progress file cursor position.

    - --- - - - - - - - -
    Parameters:
      -
    • handle (file) – open BAM file
      • -
    • offset (int) – offset of BGZF block (default: 0)
      • +
      +
      Parameters
      +
        +

      • handle (file) – open BAM file

        • +

      • offset (int) – offset of BGZF block (default: 0)

      -
    Returns:

    Complete BGZF block

    -
    Raises:

    ValueError – if the BGZF block header is malformed

    -
    + +
    Returns
    +

    Complete BGZF block

    +
    +
    Raises
    +

    ValueError – if the BGZF block header is malformed

    +
    +

    Example

    >>> bam_header = get_block(bamnostic.example_bam)
 >>> try:
@@ -688,27 +664,23 @@
 within the deflated BGZF block where the position starts. The virtual offset
 is defined as
    
 
    virtual_offset = coffset << 16 | uoffset
    
-
---
-
-
-
-
-
-
-
-
-
-
    


    Parameters:
    virtual_offset (int) – 64-bit unsigned composite byte offset
    
-
    Returns:
    an echo of the new position
    
-
    Return type:
    virtual_offset (int)
    
-
    Raises:
      
-
    • ValueError – if within block offset is more than block size
      • 
-
    • AssertionError – if the start position is not the block start position
      • 
+
      
+
      Parameters
      
+
      virtual_offset (int) – 64-bit unsigned composite byte offset
      
+
      
+
      Returns
      
+
      an echo of the new position
      
+
      
+
      Return type
      
+
      virtual_offset (int)
      
+
      
+
      Raises
      
+
        
+
      • ValueError – if within block offset is more than block size
        • 
+
      • AssertionError – if the start position is not the block start position
        • 
 
      
-
    
+
+
 
    Example
    
 
    >>> bam = bamnostic.AlignmentFile(bamnostic.example_bam, 'rb')
 >>> bam.seek(10)
@@ -727,27 +699,23 @@
 
    
 read(size=-1)[source]
    
 
    Read method for the BGZF module.
    
-
---
-
-
-
-
-
-
-
-
-
-
    


    Parameters:
    size (int) – the number of bytes to read from file. Advances the cursor.
    
-
    Returns:
    byte string of length size
    
-
    Return type:
    data (bytes)
    
-
    Raises:
      
-
    • NotImplementedError – if the user tries to read the whole file
      • 
-
    • AssertionError – if read does not return any data
      • 
+
      
+
      Parameters
      
+
      size (int) – the number of bytes to read from file. Advances the cursor.
      
+
      
+
      Returns
      
+
      byte string of length size
      
+
      
+
      Return type
      
+
      data (bytes)
      
+
      
+
      Raises
      
+
        
+
      • NotImplementedError – if the user tries to read the whole file
        • 
+
      • AssertionError – if read does not return any data
        • 
 
      
-
    
+
    
+
 
 
 
    
@@ -769,8 +737,8 @@
 seekable()[source]
 
    Return True indicating the BGZF supports random access.
    
 
    
-
    Note
    
-
    Modified from original Bio.BgzfReader: checks to see if BAM
+
    Note
    
+
    Modified from original Bio.BgzfReader: checks to see if BAM
 file has associated index file (BAI)
    
 
    
 
    
@@ -942,48 +910,40 @@
 
    
 bamnostic.bai.reg2bin(rbeg, rend)[source]
    
 
    Finds the largest superset bin of region. Numeric values taken from hts-specs
    
-
---
-
-
-
-
-
-
-
-
    


    Parameters:
      
-
    • rbeg (int) – inclusive beginning position of region
      • 
-
    • rend (int) – exclusive end position of region
      • 
+
      
+
      Parameters
      
+
        
+
      • rbeg (int) – inclusive beginning position of region
        • 
+
      • rend (int) – exclusive end position of region
        • 
 
      
-
    Returns:
    distinct bin ID for largest superset bin of region
    
-
    Return type:
    (int)
    
-
    
+
    
+
    Returns
    
+
    distinct bin ID for largest superset bin of region
    
+
    
+
    Return type
    
+
    (int)
    
+
    
+
 
 
 
    
 
    
 bamnostic.bai.reg2bins(rbeg, rend)[source]
    
 
    Generates bin ids which overlap the specified region.
    
-
---
-
-
-
-
-
-
-
-
    


    Parameters:
      
-
    • rbeg (int) – inclusive beginning position of region
      • 
-
    • rend (int) – exclusive end position of region
      • 
+
      
+
      Parameters
      
+
        
+
      • rbeg (int) – inclusive beginning position of region
        • 
+
      • rend (int) – exclusive end position of region
        • 
 
      
-
    Yields:
    (int) – bin IDs for overlapping bins of region
    
-
    Raises:
    AssertionError (Exception) – if the range is malformed or invalid
    
-
    
+
    
+
    Yields
    
+
    (int) – bin IDs for overlapping bins of region
    
+
    
+
    Raises
    
+
    AssertionError (Exception) – if the range is malformed or invalid
    
+
    
+
    
 
 
 
    
@@ -1001,84 +961,66 @@
 
    
 _io
    
 
    opened BAI file object
    
-
---
-
-
-
-
    


    Type:fileObject
    
+
    
+
    Type
    
+
    fileObject
    
+
    
+
    
 
    
 
 
    
 
    
 _LINEAR_INDEX_WINDOW
    
 
    constant of the linear interval window size
    
-
---
-
-
-
-
    


    Type:int
    
+
    
+
    Type
    
+
    int
    
+
    
+
    
 
    
 
 
    
 
    
 _UNMAP_BIN
    
 
    constant for bin ID of unmapped read stats
    
-
---
-
-
-
-
    


    Type:int
    
+
    
+
    Type
    
+
    int
    
+
    
+
    
 
    
 
 
    
 
    
 magic
    
 
    first 4 bytes of file. Must be equal to b’BAI’
    
-
---
-
-
-
-
    


    Type:bytes
    
+
    
+
    Type
    
+
    bytes
    
+
    
+
    
 
    
 
 
    
 
    
 n_refs
    
 
    number of references in BAI
    
-
---
-
-
-
-
    


    Type:int
    
+
    
+
    Type
    
+
    int
    
+
    
+
    
 
    
 
 
    
 
    
 unmapped
    
 
    dictionary of the unmapped read stats by each reference
    
-
---
-
-
-
-
    


    Type:dict
    
+
    
+
    Type
    
+
    dict
    
+
    
+
    
 
    
 
 
    
@@ -1087,56 +1029,44 @@
 
    dictionary of the current reference loaded into memory.
 It contains the a dictionary of bin IDs and their respective
 chunks, and a list of linear intervals.
    
-
---
-
-
-
-
    


    Type:None|dict
    
+
    
+
    Type
    
+
    None|dict
    
+
    
+
    
 
    
 
 
    
 
    
 ref_indices
    
 
    dictionary of reference ids and their start/stop offsets within the BAI file
    
-
---
-
-
-
-
    


    Type:dict
    
+
    
+
    Type
    
+
    dict
    
+
    
+
    
 
    
 
 
    
 
    
 n_no_coord
    
 
    if present in BAI, is the number of reads that have no coordinates
    
-
---
-
-
-
-
    


    Type:None|int
    
+
    
+
    Type
    
+
    None|int
    
+
    
+
    
 
    
 
 
    
 
    
 _last_pos
    
 
    used for indexing, the byte position of the file head.
    
-
---
-
-
-
-
    


    Type:int
    
+
    
+
    Type
    
+
    int
    
+
    
+
    
 
    
 
 
    
@@ -1150,22 +1080,21 @@
 
    Note: a special case of a chunk is in any Bin labeled as 37450.
 These bins always contain 2 chunks that provide the statistics
 of the number of reads that are unmapped to that reference.
    
-
---
-
-
-
-
-
-
-
-
    


    Parameters:n_chunks (int) – number of chunks to be unpacked from stream
    Returns:
    
-
    a list of Chunk objects with the attributes of
    
-
    chunks[i] are .voffset_beg and voffset_end
    
+
    
+
    Parameters
    
+
    n_chunks (int) – number of chunks to be unpacked from stream
    
+
    
+
    Returns
    
+
    
+
    a list of Chunk objects with the attributes of
    chunks[i] are .voffset_beg and voffset_end
    
+
    
+
    
+
    
+
    
+
    Return type
    
+
    chunks (list)
    
+
    
 
    
-
    Return type:chunks (list)
    
 
    
 
 
    
@@ -1180,18 +1109,17 @@
 
    Note: a caveat to using linear interval with long reads: A long read can
 span multiple linear intervals. As such, the current encoding could potentially shift
 the expected region of interest to the left more than expected.
    
-
---
-
-
-
-
-
-
-
-
    


    Parameters:n_int (int) – number of intervals to unpack
    Returns:list of virtual offsets for n_int number of linear intervals
    Return type:intervals (list)
    
+
    
+
    Parameters
    
+
    n_int (int) – number of intervals to unpack
    
+
    
+
    Returns
    
+
    list of virtual offsets for n_int number of linear intervals
    
+
    
+
    Return type
    
+
    intervals (list)
    
+
    
+
    
 
    
 
 
    
@@ -1213,24 +1141,24 @@
 
    As a secondary feature, this function will also quickly seek over regions for
 the purposes of documenting the start and stop byte offsets of a given reference
 block within the file. This is invoked by setting idx=True
    
-
---
-
-
-
-
-
-
-
-
-
-
    


    Parameters:n_int (int) – number of bins to be unpacked from stream
    Returns:
    
-
    None if just indexing the index file or a dictionary
    
-
    of bin_id: chunks pairs
    
+
    
+
    Parameters
    
+
    n_int (int) – number of bins to be unpacked from stream
    
+
    
+
    Returns
    
+
    
+
    None if just indexing the index file or a dictionary
    of bin_id: chunks pairs
    
+
    
+
    
+
    
+
    
+
    Return type
    
+
    bins (None | dict)
    
+
    
+
    Raises
    
+
    AssertionError (Exception) – if bin 37450 does not contain 2 chunks exactly
    
+
    
 
    
-
    Return type:bins (None | dict)
    Raises:AssertionError (Exception) – if bin 37450 does not contain 2 chunks exactly
    
 
    
 
 
    
@@ -1247,30 +1175,26 @@
 loaded. Because of this constant loading, functools.lru_cache was applied to cache recently
 used reference blocks to speed up computation. It is assumed that when querying is done, most
 users are looking and just a few references at a time.
    
-
---
-
-
-
-
-
-
-
-
-
-
    


    Parameters:
      
-
    • ref_id (None|int) – used for random access or indexing the BAI
      • 
-
    • idx (bool) – Flag for setting whether or not to run an index of the BAI
      • 
+
      
+
      Parameters
      
+
        
+
      • ref_id (None|int) – used for random access or indexing the BAI
        • 
+
      • idx (bool) – Flag for setting whether or not to run an index of the BAI
        • 
 
      
-
    Returns:
    namedtuple containing the byte offsets of the reference start, stop, and number of bins
+
+
    Returns
    
+
    namedtuple containing the byte offsets of the reference start, stop, and number of bins
 or
 Ref: namedtuple containing a dictionary of bins and list of linear intervals
    
-
    Return type:
    RefIdx
    
-
    Raises:
    AssertionError (Exception) – if, when random access is used, the current reference offset
-does not match indexed reference offset.
    
-
    
+
+
    Return type
    
+
    RefIdx
    
+
    
+
    Raises
    
+
    AssertionError (Exception) – if, when random access is used, the current reference offset
+    does not match indexed reference offset.
    
+
    
+
    
 
 
 
    
@@ -1278,58 +1202,49 @@
 query(ref_id, start, stop=-1)[source]
 
    Main query function for determining seek offset to BAM section that
 AlignedRead objects from specified region start
    
-
---
-
-
-
-
-
-
-
-
    


    Parameters:
      
-
    • ref (int) – which reference/chromosome TID
      • 
-
    • start (int) – left most bp position of region (zero-based)
      • 
-
    • stop (int) – right most bp position of region (zero-based)
      • 
+
      
+
      Parameters
      
+
        
+
      • ref (int) – which reference/chromosome TID
        • 
+
      • start (int) – left most bp position of region (zero-based)
        • 
+
      • stop (int) – right most bp position of region (zero-based)
        • 
 
      
-
    Returns:
    
-
    the voffset_beg of the first chunk given the chunk’s voffset_end
    
-
    is greater than the voffset of the linear index that overlaps
+
    
+
    Returns
    
+
    
+
    the voffset_beg of the first chunk given the chunk’s voffset_end
    is greater than the voffset of the linear index that overlaps
 the region of interest’s start offset
    
 
    
 
    
 
    
-
    Return type:
    (int)
    
-
    
+
    
+
    Return type
    
+
    (int)
    
+
    
+
    
 
 
 
    
 
    
 seek(offset=None, whence=0)[source]
    
 
    Simple seek function for binary files
    
-
---
-
-
-
-
-
-
-
-
    


    Parameters:
      
-
    • offset (None|int) – byte offset from whence to move the file head to.
      • 
-
    • whence (int) – 0 := from start of file, 1:= from current position, 2:= from end of file
      • 
+
      
+
      Parameters
      
+
        
+
      • offset (None|int) – byte offset from whence to move the file head to.
        • 
+
      • whence (int) – 0 := from start of file, 1:= from current position, 2:= from end of file
        • 
 
      
-
    Returns:
    new byte position of file head
    
-
    Return type:
    (int)
    
-
    
-
    
-
    Raise:
    
-
    ValueError (Exception): if the offset is not an integer or is not provided
    
+
    
+
    Returns
    
+
    new byte position of file head
    
+
    
+
    Return type
    
+
    (int)
    
+
    
+
    
+
    
+
    Raise:
    ValueError (Exception): if the offset is not an integer or is not provided
    
+
    
 
    
 
 
@@ -1337,34 +1252,31 @@
 
    
 read(size=-1)[source]
    
 
    Simple read function for binary files
    
-
---
-
-
-
-
-
-
-
-
    


    Parameters:size (int) – number of bytes to read in (default: -1 –whole file)
    Returns:the number of bytes read from file
    Return type:(bytes)
    
+
    
+
    Parameters
    
+
    size (int) – number of bytes to read in (default: -1 –whole file)
    
+
    
+
    Returns
    
+
    the number of bytes read from file
    
+
    
+
    Return type
    
+
    (bytes)
    
+
    
+
    
 
    
 
 
    
 
    
 tell()[source]
    
 
    Simple tell function for reporting byte position of file head
    
-
---
-
-
-
-
-
-
    


    Returns:byte position of file head
    Return type:(int)
    
+
    
+
    Returns
    
+
    byte position of file head
    
+
    
+
    Return type
    
+
    (int)
    
+
    
+
    
 
    
 
 
@@ -1394,23 +1306,19 @@
 
    
 bamnostic.utils.format_warnings(message, category, filename, lineno, file=None, line=None)[source]
    
 
    Sets STDOUT warnings
    
-
---
-
-
-
-
-
-
    


    Parameters:
      
-
    • message – the unformatted warning message being reported
      • 
-
    • category (str) – the level of warning (handled by warnings module)
      • 
-
    • filename (str) – filename for logging purposes (defaults to STDOUT)
      • 
-
    • lineno (int) – where the error occurred.
      • 
+
      
+
      Parameters
      
+
        
+
      • message – the unformatted warning message being reported
        • 
+
      • category (str) – the level of warning (handled by warnings module)
        • 
+
      • filename (str) – filename for logging purposes (defaults to STDOUT)
        • 
+
      • lineno (int) – where the error occurred.
        • 
 
      
-
    Returns:
    formatted warning string
    
-
    
+
    
+
    Returns
    
+
    formatted warning string
    
+
    
+
 
 
 
    
@@ -1446,36 +1354,36 @@
 flags are used for read filtering and QC. The flags are described below.
 Additionally, they can be found here
    
 
    Any given read’s flag is determined by the or (|) operand of all appropriate bit flags.
    
-
---
-
-
-
-
-
-
-
-
-
-
    


    Parameters:flag_code (int) – either a standalone integer/bit flag or the read object itself
    Returns:list of flag and flag description tuples.
    Return type:(list of tuple)
    Raises:ValueError – if provided flag is not a valid entry
    
+
    
+
    Parameters
    
+
    flag_code (int) – either a standalone integer/bit flag or the read object itself
    
+
    
+
    Returns
    
+
    list of flag and flag description tuples.
    
+
    
+
    Return type
    
+
    (list of tuple)
    
+
    
+
    Raises
    
+
    ValueError – if provided flag is not a valid entry
    
+
    
+
    
 
    Example
    
 
    If a flag is 516 it is comprised of flag 4 and flag 512
    
 
    >>> flag_decode(516)
 [(4, 'read unmapped'), (512, 'QC fail')]
 
    
 
    
-
+
    ---+++
-
-
-
-
+
+
+
+
    
 






 
    IntBitDescription
    Int
    Bit
    Description
    		
 
    
     
 
    
@@ -1513,8 +1421,8 @@
 
    The second form a submission can take is through positional arguments. Just like
 keyword, but ordered such that it makes up a genomic region of interest.
    
 
    
-
    Note
    
-
    Positional arguments make utilizing the tid parameter difficult since it is
+
    Note
    
+
    Positional arguments make utilizing the tid parameter difficult since it is
 the 5th argument of the function signature.
    
 
    
 
    The third form a submission can take is through using a SAM-formatted string. An
@@ -1525,31 +1433,27 @@
 start position (be it the whole reference or a specific spot on the reference). Setting
 this to True (default: False) will pull all reads to the end of the reference or file,
 whichever is first.
    
-
---
-
-
-
-
-
-
-
-
-
-
    


    Parameters:
      
-
    • contig (str) – name of reference/contig
      • 
-
    • start (int) – start position of region of interest (0-based)
      • 
-
    • stop (int) – stop position of region of interest (0-based)
      • 
-
    • region (str) – SAM region formatted string. Accepts tab-delimited values as well
      • 
-
    • tid (int) – the refID or target id of a reference/contig
      • 
-
    • until_eof (bool) – iterate until end of file (default: False)
      • 
+
      
+
      Parameters
      
+
        
+
      • contig (str) – name of reference/contig
        • 
+
      • start (int) – start position of region of interest (0-based)
        • 
+
      • stop (int) – stop position of region of interest (0-based)
        • 
+
      • region (str) – SAM region formatted string. Accepts tab-delimited values as well
        • 
+
      • tid (int) – the refID or target id of a reference/contig
        • 
+
      • until_eof (bool) – iterate until end of file (default: False)
        • 
 
      
-
    Returns:
    region of interest formatted as an object with named attributes.
    
-
    Return type:
    query (bamnostic.utils.Roi)
    
-
    Raises:
    ValueError – if two synonym keywords are set, but contradict each other
    
-
    
+
+
    Returns
    
+
    region of interest formatted as an object with named attributes.
    
+
    
+
    Return type
    
+
    query (bamnostic.utils.Roi)
    
+
    
+
    Raises
    
+
    ValueError – if two synonym keywords are set, but contradict each other
    
+
    
+
    
 
    Examples
    
 
    # Keyword-based
 >>> parse_region(contig = ‘chr1’, start = 10, stop = 100)
@@ -1586,21 +1490,17 @@
 the format string. Additionally, it can process a file object or byte
 stream and implement a read or slice (respectively). Mainly, this is a
 quality of life function.
    
-
---
-
-
-
-
-
-
    


    Parameters:
      
-
    • fmt (str) – the string format of the binary data to be unpacked
      • 
-
    • _io – built-in binary format reader (default: io.BufferedRandom)
      • 
+
      
+
      Parameters
      
+
        
+
      • fmt (str) – the string format of the binary data to be unpacked
        • 
+
      • _io – built-in binary format reader (default: io.BufferedRandom)
        • 
 
      
-
    Returns:
    unpacked contents from _io based on fmt string
    
-
    
+
+
    Returns
    
+
    unpacked contents from _io based on fmt string
    
+
    
+
 
 
 
    
@@ -1658,14 +1558,11 @@
 
    
 get(key)[source]
    
 
    Basic getter that renews LRU status upon inspection
    
-
---
-
-
-
-
    


    Parameters:key (str) – immutable dictionary key
    
+
    
+
    Parameters
    
+
    key (str) – immutable dictionary key
    
+
    
+
    
 
    
 
 
    
@@ -1673,14 +1570,11 @@
 update(others)[source]
 
    Same as a regular dict.update, however, since pypy’s dict.update
 doesn’t go through dict.__setitem__, this is used to ensure it does
    
-
---
-
-
-
-
    


    Parameters:others (iterable) – a dictionary or iterable containing key/value pairs
    
+
    
+
    Parameters
    
+
    others (iterable) – a dictionary or iterable containing key/value pairs
    
+
    
+
    
 
    
 
 
    
@@ -1696,20 +1590,20 @@
 
    
 bamnostic.utils.parse_cigar(cigar_str)[source]
    
 
    Parses a CIGAR string and turns it into a list of tuples
    
-
---
-
-
-
-
-
-
-
-
-
-
    


    Parameters:cigar_str (str) – the CIGAR string as shown in SAM entry
    Returns:list of tuples of CIGAR operations (by id) and number of operations
    Return type:cigar_array (list)
    Raises:ValueError – if CIGAR operation is invalid
    
+
    
+
    Parameters
    
+
    cigar_str (str) – the CIGAR string as shown in SAM entry
    
+
    
+
    Returns
    
+
    list of tuples of CIGAR operations (by id) and number of operations
    
+
    
+
    Return type
    
+
    cigar_array (list)
    
+
    
+
    Raises
    
+
    ValueError – if CIGAR operation is invalid
    
+
    
+
    
 
    Examples
    
 
    >>> parse_cigar('3M1I3M1D5M') # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
 [(('BAM_CMATCH', 0), 3), ..., (('BAM_CMATCH', 0), 5)]
@@ -1721,50 +1615,46 @@
 
    
 bamnostic.utils.check_cigar_arg(cigar)[source]
    
 
    Checks to make sure CIGAR arugment is valid.
    
-
---
-
-
-
-
-
-
-
-
-
-
    


    Parameters:argument (str or list) – CIGAR string (pre-formatted or raw)
    Returns:CIGAR re-formatted as a list
    Return type:(list)
    Raises:ValueError – if CIGAR is not a string or pre-formatted list
    
+
    
+
    Parameters
    
+
    argument (str or list) – CIGAR string (pre-formatted or raw)
    
+
    
+
    Returns
    
+
    CIGAR re-formatted as a list
    
+
    
+
    Return type
    
+
    (list)
    
+
    
+
    Raises
    
+
    ValueError – if CIGAR is not a string or pre-formatted list
    
+
    
+
    
 
    
 
 
    
 
    
 bamnostic.utils.cigar_changes(seq, cigar)[source]
    
-
    
-
    Recreates the reference sequence to the extent that the CIGAR string can
    
-
    represent.
    
+
    
+
    Recreates the reference sequence to the extent that the CIGAR string can
    represent.
    
+
    
 
    
-
---
-
-
-
-
-
-
-
-
-
-
    


    Parameters:
      
-
    • seq (str) – aligned segment sequence
      • 
-
    • cigar (list) – list of tuples of cigar operations (by id) and number of operations
      • 
+
      
+
      Parameters
      
+
        
+
      • seq (str) – aligned segment sequence
        • 
+
      • cigar (list) – list of tuples of cigar operations (by id) and number of operations
        • 
 
      
-
    Returns:
    a version of the aligned segment’s reference             sequence given the changes reflected in the cigar string
    
-
    Return type:
    cigar_formatted_ref (str)
    
-
    Raises:
    ValueError – if CIGAR operation is invalid
    
-
    
+
    
+
    Returns
    
+
    a version of the aligned segment’s reference             sequence given the changes reflected in the cigar string
    
+
    
+
    Return type
    
+
    cigar_formatted_ref (str)
    
+
    
+
    Raises
    
+
    ValueError – if CIGAR operation is invalid
    
+
    
+
    
 
    Examples
    
 
    >>> cigar_changes('ACTAGAATGGCT', '3M1I3M1D5M')
 'ACTGAATGGCT'
@@ -1784,31 +1674,27 @@
 
    Recreates the reference sequence of a given alignment to the extent that the
 MD tag can represent.
    
 
    
-
    Note
    
-
    Used in conjunction with cigar_changes to recreate the
+
    Note
    
+
    Used in conjunction with cigar_changes to recreate the
 complete reference sequence
    
 
    
-
---
-
-
-
-
-
-
-
-
-
-
    


    Parameters:
      
-
    • seq (str) – aligned segment sequence
      • 
-
    • md_tag (str) – MD tag for associated sequence
      • 
+
      
+
      Parameters
      
+
        
+
      • seq (str) – aligned segment sequence
        • 
+
      • md_tag (str) – MD tag for associated sequence
        • 
 
      
-
    Returns:
    a version of the aligned segment’s reference sequence given             the changes reflected in the MD tag
    
-
    Return type:
    ref_seq (str)
    
-
    Raises:
    ValueError – if MD tag is None
    
-
    
+
    
+
    Returns
    
+
    a version of the aligned segment’s reference sequence given             the changes reflected in the MD tag
    
+
    
+
    Return type
    
+
    ref_seq (str)
    
+
    
+
    Raises
    
+
    ValueError – if MD tag is None
    
+
    
+
    
 
    Example
    
 
    >>> md_changes('CTTATATTGGCCTT', '3C4AT4')
 'CTTCTATTATCCTT'
@@ -1824,18 +1710,17 @@
 with the aligned segment. This is done without the need for looking up
 the reference genome. Example reads, MD tags, and CIGAR strings taken from
 David Tang’s Blog.
    
-
---
-
-
-
-
-
-
-
-
    


    Returns:generated reference sequence
    Return type:(str)
    Raises:KeyError – if read does not contain MD tag
    
+
    
+
    Returns
    
+
    generated reference sequence
    
+
    
+
    Return type
    
+
    (str)
    
+
    
+
    Raises
    
+
    KeyError – if read does not contain MD tag
    
+
    
+
    
 
    Examples
    
 
    # Only mismatches
 >>> seq = ‘CGATACGGGGACATCCGGCCTGCTCCTTCTCACATG’
@@ -1870,23 +1755,19 @@
 
    Any clipping results in the removal of those bases. If an insertion is seen in
 the CIGAR, those bases are removed from the sequence. If a deletion is seen in
 the CIGAR, those bases are padded with a period (‘.’) symbol.
    
-
---
-
-
-
-
-
-
    


    Parameters:
      
-
    • seq (str) – string sequence of the aligned segment.
      • 
-
    • cigar (str) – the cigar string or cigartuple of the aligned segment.
      • 
-
    • start_pos (int) – the first aligned position of the read
      • 
-
    • qualities (array.array) – base quality array from read
      • 
+
      
+
      Parameters
      
+
        
+
      • seq (str) – string sequence of the aligned segment.
        • 
+
      • cigar (str) – the cigar string or cigartuple of the aligned segment.
        • 
+
      • start_pos (int) – the first aligned position of the read
        • 
+
      • qualities (array.array) – base quality array from read
        • 
 
      
-
    Yields:
    (tuple of str and int) – nucleotide base and index position of that base relative to reference
    
-
    
+
+
    Yields
    
+
    (tuple of str and int) – nucleotide base and index position of that base relative to reference
    
+
    
+
 
    Example
    
 
    >>> seq = 'AGTGATGGGAGGATGTCTCGTCTGTGAGTTACAGCA'
 >>> cigar = '2M1I7M6D26M'
diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html
index af4bc3f..e2614ea 100644
--- a/docs/build/html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -9,7 +9,7 @@
   
   
   
-  Index — bamnostic 1.0.9 documentation
+  Index — bamnostic 1.0.10 documentation
   
 
   
@@ -60,7 +60,7 @@
             
             
               
    
-                1.0.9
+                1.0.10
               
    
             
           
diff --git a/docs/build/html/index.html b/docs/build/html/index.html
index c177f86..62ca27c 100644
--- a/docs/build/html/index.html
+++ b/docs/build/html/index.html
@@ -8,7 +8,7 @@
   
   
   
-  Welcome to bamnostic’s documentation! — bamnostic 1.0.9 documentation
+  Welcome to bamnostic’s documentation! — bamnostic 1.0.10 documentation
   
 
   
@@ -60,7 +60,7 @@
             
             
               
    
-                1.0.9
+                1.0.10
               
    
             
           
@@ -160,8 +160,8 @@ 
    Welcome to bamnostic’s documentation!
-
    Note
    
-
    CRAM format is not supported at this time.
    
+
    Note
    
+
    CRAM format is not supported at this time.
    
 
    
 
    
 
    Contents:
    
@@ -210,9 +210,9 @@ 
    Welcome to bamnostic’s documentation!
 
    Indices and tables
    
 
 
    
 
diff --git a/docs/build/html/install.html b/docs/build/html/install.html
index 1ae0708..7437134 100644
--- a/docs/build/html/install.html
+++ b/docs/build/html/install.html
@@ -8,7 +8,7 @@
   
   
   
-  Installation — bamnostic 1.0.9 documentation
+  Installation — bamnostic 1.0.10 documentation
   
 
   
@@ -61,7 +61,7 @@
             
             
               
    
-                1.0.9
+                1.0.10
               
    
             
           
@@ -166,41 +166,41 @@ 
    Installation
 
    Through the conda package manager (Anaconda Cloud)
    
-
    # first, add the conda-forge channel to your conda build
-conda config --add channels conda-forge
+
    # first, add the conda-forge channel to your conda build
+conda config --add channels conda-forge
 
 # now bamnostic is available for install
-conda install bamnostic
+conda install bamnostic
 
    
 
    
 
    
 
    
 
    Through the Python Package Index (PyPI)
    
-
    pip install bamnostic
+
    pip install bamnostic
 
 # or, if you don't have superuser access
-pip install --user bamnostic
+pip install --user bamnostic
 
    
 
    
 
    
 
    
 
    Through pip+Github
    
-
    # again, use --user if you don't have superuser access
-pip install -e git+https://github.com/betteridiot/bamnostic.git
+
    # again, use --user if you don't have superuser access
+pip install -e git+https://github.com/betteridiot/bamnostic.git
 
 # or, if you don't have superuser access
-pip install --user -e git+https://github.com/betteridiot/bamnostic.git
+pip install --user -e git+https://github.com/betteridiot/bamnostic.git
 
    
 
    
 
    
 
    
 
    Traditional GitHub clone
    
-
    git clone https://github.com/betteridiot/bamnostic.git
-cd bamnostic
-pip install -e .
+
    git clone https://github.com/betteridiot/bamnostic.git
+cd bamnostic
+pip install -e .
 
 # or, if you don't have superuser access
-pip install --user -e .
+pip install --user -e .
 
    
 
    
 
    
diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
index d4d813cbfea5292332592792e461e7883806591d..24106a0645fd88634a5f7e664060805c85d7894c 100644
GIT binary patch
delta 13
UcmZqTZ04Nc$Yf}+(aC`Y02){Wg8%>k

delta 12
TcmZqXY~q~Y$Y{CI*?|QB7jpw!

diff --git a/docs/build/html/py-modindex.html b/docs/build/html/py-modindex.html
index 093dbca..8ea2578 100644
--- a/docs/build/html/py-modindex.html
+++ b/docs/build/html/py-modindex.html
@@ -8,7 +8,7 @@
   
   
   
-  Python Module Index — bamnostic 1.0.9 documentation
+  Python Module Index — bamnostic 1.0.10 documentation
   
 
   
@@ -62,7 +62,7 @@
             
             
               
    
-                1.0.9
+                1.0.10
               
    
             
           
@@ -169,22 +169,28 @@ 
    Python Module Index
    
        
        bamnostic
        
-     
+     
+       
+       
+       bamnostic
+       
+     
        
           
        bamnostic.bai
        
-     
+     
        
           
        bamnostic.bgzf
        
-     
+     
        
           
        bamnostic.core
        
-     
+     
        
           
        bamnostic.utils
diff --git a/docs/build/html/quickstart.html b/docs/build/html/quickstart.html
index fb5f915..a6f583d 100644
--- a/docs/build/html/quickstart.html
+++ b/docs/build/html/quickstart.html
@@ -8,7 +8,7 @@
   
   
   
-  Quickstart — bamnostic 1.0.9 documentation
+  Quickstart — bamnostic 1.0.10 documentation
   
 
   
@@ -61,7 +61,7 @@
             
             
               
    
-                1.0.9
+                1.0.10
               
    
             
           
@@ -179,12 +179,12 @@ 
    Quickstartpysam. As such it has
 much the same API as pysam with regard to BAM-related operations.
    
 
    
-
    Note
    
-
    the pileup() method is not supported at this time.
    
+
    Note
    
+
    the pileup() method is not supported at this time.
    
 
    
 
    
 
    Importing bamnostic
    
-
    import bamnostic as bs
+
    import bamnostic as bs
 
    
 
    
 
    
@@ -196,7 +196,7 @@ 
    Loading your BAM filebamnostic.example_bam, which is a just a string path to the BAM file
 within the package.
    
-
    >>> bam = bs.AlignmentFile(bs.example_bam, 'rb')
+
    >>> bam = bs.AlignmentFile(bs.example_bam, 'rb')
 
    
 
    
 
    
@@ -206,14 +206,14 @@ 
    Get the header
    >>> bam.header
+
    >>> bam.header
 {0: ('chr1', 1575), 1: ('chr2', 1584)}
 
    
 
    
 
    
 
    
 
    Data validation through head()
    
-
    >>>bam.head(n=2)
+
    >>>bam.head(n=2)
 [EAS56_57:6:190:289:82  69  chr1    100 0   *   =   100 0   CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA <<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<; MF:C:192,
  EAS56_57:6:190:289:82  137 chr1    100 73  35M =   100 0   AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC <<<<<<;<<<<<<<<<<;<<;<<<<;8<6;9;;2; MF:C:64 Aq:C:0  NM:C:0  UQ:C:0  H0:C:1  H1:C:0]
 
    
@@ -221,31 +221,31 @@ 
    Data validation through 
 
    
 
    Getting the next read
    
-
    >>> print(next(bam))
+
    >>> print(next(bam))
 EAS56_57:6:190:289:82       69      chr1    100     0       *       =       100     0       CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA     <<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<;     MF:C:192
 
    
 
    
 
    
 
    
 
    Exploring a read
    
-
    # Using a more complex read
+
    # Using a more complex read
 >>> for complex_read in bam:
 ...     if complex_read.read_name == 'EAS218_4:1:48:9:409':
-...         print(complex_read)
+...         print(complex_read)
 ...         break
 EAS218_4:1:48:9:409 99      chr1    271     75      18M5I12M        =       464     228     GTTTAGTGCCTTTGTTCACATAGACCCCCTTGCAA     <<<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<     MF:C:130        Aq:C:75 NM:C:0  UQ:C:0  H0:C:0  H1:C:0
 
    
 
    
 
    There are, essentially, 3 contexts of a given read:
    
 
      
-
    1. (raw) The raw read
      2. 
-
    2. (aligned) The sequence that aligns (including insertions but not clipping)
      3. 
-
    3. (reference) The sequence that aligns to the reference only (excluding clipping and insertions)
      4. 
+
    4. (raw) The raw read
      5. 
+
    5. (aligned) The sequence that aligns (including insertions but not clipping)
      6. 
+
    6. (reference) The sequence that aligns to the reference only (excluding clipping and insertions)
      7. 
 
    
 
    Let’s explore an example of those different contexts.
    
 
    
 
    Read Name
    
-
    >>> print(complex_read.read_name)
+
    >>> print(complex_read.read_name)
 EAS218_4:1:48:9:409
 
    
 
    
@@ -259,22 +259,22 @@ 
    0-based Start Position (raw, aligned, reference)
    >>> print(complex_read.pos, complex_read.query_alignment_start, complex_read.reference_start)
+
    >>> print(complex_read.pos, complex_read.query_alignment_start, complex_read.reference_start)
 270 270 270
 
    
 
    
 
    
 
    
 
    CIGAR & QUAL Strings
    
-
    >>> print(complex_read.cigarstring)
+
    >>> print(complex_read.cigarstring)
 18M5I12M
 
 # ASCII-encoded and offset quality scores
->>> print(complex_read.qual)
+>>> print(complex_read.qual)
 <<<<<<<<<<<<<:<<<<<<<<<<<<<<<<<<<<<
 
 # Decoded and raw
->>> print(complex_read.query_qualities)
+>>> print(complex_read.query_qualities)
 array('B', [27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27])
 
    
 
    
@@ -283,19 +283,19 @@ 
    CIGAR & QUAL StringsSequence Length (raw, aligned, reference)
    
 
    Since the CIGAR string contains an insertion of 5 bases, the read’s reference
 length should be 5 bases shorter than the query.
    
-
    >>> print(complex_read.query_length, complex_read.query_alignment_length, complex_read.reference_length)
+
    >>> print(complex_read.query_length, complex_read.query_alignment_length, complex_read.reference_length)
 35 35 30
 
    
 
    
 
    
 
    
 
    Nucleotide Sequence
    
-
    # nucleotide sequence (raw)
->>> print(complex_read.query_sequence)
+
    # nucleotide sequence (raw)
+>>> print(complex_read.query_sequence)
 GTTTAGTGCCTTTGTTCACATAGACCCCCTTGCAA
 
 # nucleotide sequence (aligned)
->>> print(first_read.query_alignment_sequence)
+>>> print(first_read.query_alignment_sequence)
 GTTTAGTGCCTTTGTTCACATAGACCCCCTTGCAA
 
 # the reference sequence cannot be generated because the read does not have
@@ -305,7 +305,7 @@ 
    Nucleotide Sequence
 
    Read Flag and Decoded Flag
    
-
    >>> print(first_read.flag)
+
    >>> print(first_read.flag)
 69
 
 # decoded FLAG
@@ -317,11 +317,11 @@ 
    Read Flag and Decoded Flag
 
    Serial Access
    
-
    >>> bam = bs.AlignmentFile(bs.example_path, 'rb')
+
    >>> bam = bs.AlignmentFile(bs.example_path, 'rb')
 >>> for i, read in enumerate(bam):
 ...    if i >= 3:
 ...        break
-...    print(read)
+...    print(read)
 
 EAS56_57:6:190:289:82       137     chr1    100     73      35M     =       100     0       AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC     <<<<<<;<<<<<<<<<<;<<;<<<<;8<6;9;;2;     MF:C:64 Aq:C:0  NM:C:0  UQ:C:0  H0:C:1  H1:C:0
 EAS51_64:3:190:727:308      99      chr1    103     99      35M     =       263     195     GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG     <<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844     MF:C:18 Aq:C:73 NM:C:0  UQ:C:0  H0:C:1  H1:C:0
@@ -331,11 +331,11 @@ 
    Serial Access
 
    Random Access
    
-
    >>> bam = bs.AlignmentFile(bs.example_path, 'rb')
+
    >>> bam = bs.AlignmentFile(bs.example_path, 'rb')
 >>> for i, read in enumerate(bam.fetch('chr2', 1, 100)):
 ...    if i >= 3:
 ...        break
-...    print(read)
+...    print(read)
 
 B7_591:8:4:841:340  73      chr2    1       99      36M     *       0       0       TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAA    <<<<<<<<;<<<<<<<<;<<<<<;<;:<<<<<<<;;    MF:C:18 Aq:C:77 NM:C:0  UQ:C:0  H0:C:1  H1:C:0
 EAS54_67:4:142:943:582      73      chr2    1       99      35M     *       0       0       TTCAAATGAACTTCTGTAATTGAAAAATTCATTTA     <<<<<<;<<<<<<:<<;<<<<;<<<;<<<:;<<<5     MF:C:18 Aq:C:41 NM:C:0  UQ:C:0  H0:C:1  H1:C:0
diff --git a/docs/build/html/search.html b/docs/build/html/search.html
index 6090020..706206b 100644
--- a/docs/build/html/search.html
+++ b/docs/build/html/search.html
@@ -8,7 +8,7 @@
   
   
   
-  Search — bamnostic 1.0.9 documentation
+  Search — bamnostic 1.0.10 documentation
   
 
   
@@ -60,7 +60,7 @@
             
             
               
    
-                1.0.9
+                1.0.10
               
    
             
           
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index f1bbb6e..226306a 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
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package","Welcome to bamnostic\u2019s documentation!","Installation","Quickstart","Citation and Support"],titleterms:{"import":3,access:3,align:[0,3],anaconda:2,bai:0,bam:[0,3],bamnost:[0,1,3,4],base:3,bgzf:0,binari:0,cigar:3,citat:4,clone:2,cloud:2,conda:2,core:0,data:3,decod:3,document:1,explor:3,file:[0,3],flag:3,get:3,github:2,handler:0,head:3,header:3,index:[0,2],indic:1,instal:2,length:3,load:3,manag:2,map:0,modul:0,name:3,next:3,nucleotid:3,packag:[0,2],pip:2,posit:3,pypi:2,python:2,qual:3,quickstart:3,random:3,raw:3,read:3,refer:3,sequenc:3,serial:3,start:3,string:3,support:4,tabl:1,through:[2,3],tradit:2,util:0,valid:3,welcom:1,your:3}})
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diff --git a/docs/build/html/support.html b/docs/build/html/support.html
index f26a7ea..01caf33 100644
--- a/docs/build/html/support.html
+++ b/docs/build/html/support.html
@@ -8,7 +8,7 @@
   
   
   
-  Citation and Support — bamnostic 1.0.9 documentation
+  Citation and Support — bamnostic 1.0.10 documentation
   
 
   
@@ -60,7 +60,7 @@
             
             
               
    
-                1.0.9
+                1.0.10
               
    
             
           
@@ -165,7 +165,8 @@ 
    Citationhttps://doi.org/10.21105/joss.00826
    
+
    Sherman MD and Mills RE, (2018). BAMnostic: an OS-agnostic toolkit for genomic sequence analysis . Journal of Open Source Software, 3(28), 826, https://doi.org/10.21105/joss.00826
    
+
    
 
    Also, if you have not already done so, also consider citing Li et al (2009).
    
 
    
 
    
diff --git a/docs/paper/codemeta.json b/docs/paper/codemeta.json
index 3bcaa80..8611f18 100644
--- a/docs/paper/codemeta.json
+++ b/docs/paper/codemeta.json
@@ -37,8 +37,8 @@
   "description": "BAMnostic: an OS-agnostic toolkit for genomic sequence analysis",
   "keywords": "BAM, pysam, genomics, genetics, htslib, samtools",
   "license": "https://github.com/betteridiot/bamnostic/blob/master/LICENSE",
-  "softwareVersion": "v1.0.9",
-  "version": "v1.0.9",
+  "softwareVersion": "v1.0.10",
+  "version": "v1.0.10",
   "readme": "https://github.com/betteridiot/bamnostic/blob/master/README.md",
   "buildInstructions": "https://github.com/betteridiot/bamnostic/blob/master/README.md",
   "issueTracker": "https://github.com/betteridiot/bamnostic/issues",
diff --git a/setup.py b/setup.py
index 0c64524..2557bd9 100644
--- a/setup.py
+++ b/setup.py
@@ -41,7 +41,7 @@ def readme():
     cmdclass = {'test' : PyTest},
     packages=['bamnostic', 'tests'],
     package_dir={'bamnostic': './bamnostic', 'tests': './tests'},
-    package_data={'bamnostic': ['data/*', 'LICENSE', 'CONTRIBUTING.md', 'CODE_OF_CONDUCT.md']},
+    package_data={'bamnostic': ['data/*', 'LICENSE', 'CONTRIBUTING.md', 'CODE_OF_CONDUCT.md', 'version']},
     classifiers=[
         'Development Status :: 5 - Production/Stable',
         'Intended Audience :: Developers',
diff --git a/version b/version
index e5a4a5e..437d26b 100644
--- a/version
+++ b/version
@@ -1 +1 @@
-1.0.9
\ No newline at end of file
+1.0.10
\ No newline at end of file