From 9ad0ef5d127fdde305bce1a8680b8b85888773c0 Mon Sep 17 00:00:00 2001 From: Retype GitHub Action Date: Mon, 8 Jul 2024 13:47:35 +0000 Subject: [PATCH] Refreshes Retype-generated documentation. Process triggered by pdimens. --- 404.html | 8 ++++---- blog/filteringsnps/index.html | 10 +++++----- blog/index.html | 8 ++++---- blog/softwareenvironments/index.html | 10 +++++----- categories/guides/index.html | 8 ++++---- categories/index.html | 8 ++++---- commonoptions/index.html | 10 +++++----- development/index.html | 10 +++++----- haplotagdata/index.html | 8 ++++---- index.html | 8 ++++---- install/index.html | 10 +++++----- issues/index.html | 10 +++++----- modules/align/bwa/index.html | 10 +++++----- modules/align/ema/index.html | 10 +++++----- modules/align/index.html | 8 ++++---- modules/align/strobe/index.html | 10 +++++----- modules/deconvolve/index.html | 14 +++++++------- modules/demultiplex/index.html | 10 +++++----- modules/impute/index.html | 10 +++++----- modules/other/index.html | 10 +++++----- modules/phase/index.html | 10 +++++----- modules/preflight/index.html | 10 +++++----- modules/qc/index.html | 10 +++++----- modules/simulate/index.html | 8 ++++---- .../simulate/simulate-linkedreads/index.html | 10 +++++----- modules/simulate/simulate-variants/index.html | 10 +++++----- modules/snp/index.html | 10 +++++----- modules/sv/index.html | 8 ++++---- modules/sv/leviathan/index.html | 10 +++++----- modules/sv/naibr/index.html | 10 +++++----- resources/js/config.js | 2 +- sitemap.xml.gz | Bin 566 -> 566 bytes snakemake/index.html | 10 +++++----- software/index.html | 8 ++++---- 34 files changed, 153 insertions(+), 153 deletions(-) diff --git a/404.html b/404.html index 431efc55a..708b4196c 100644 --- a/404.html +++ b/404.html @@ -4,7 +4,7 @@ - + @@ -29,11 +29,11 @@ - + - + - +
diff --git a/blog/filteringsnps/index.html b/blog/filteringsnps/index.html index 548efafbb..32e6bf068 100644 --- a/blog/filteringsnps/index.html +++ b/blog/filteringsnps/index.html @@ -4,7 +4,7 @@ - + @@ -37,12 +37,12 @@ - + - + - - + +
diff --git a/blog/index.html b/blog/index.html index e7568d482..ddc442e3e 100644 --- a/blog/index.html +++ b/blog/index.html @@ -4,7 +4,7 @@ - + @@ -32,11 +32,11 @@ - + - + - +
diff --git a/blog/softwareenvironments/index.html b/blog/softwareenvironments/index.html index d55cc592f..8dd722ecc 100644 --- a/blog/softwareenvironments/index.html +++ b/blog/softwareenvironments/index.html @@ -4,7 +4,7 @@ - + @@ -37,12 +37,12 @@ - + - + - - + +
diff --git a/categories/guides/index.html b/categories/guides/index.html index a40e8d9d9..bd2aee033 100644 --- a/categories/guides/index.html +++ b/categories/guides/index.html @@ -4,7 +4,7 @@ - + @@ -29,11 +29,11 @@ - + - + - +
diff --git a/categories/index.html b/categories/index.html index fdfaa7ef8..848134da6 100644 --- a/categories/index.html +++ b/categories/index.html @@ -4,7 +4,7 @@ - + @@ -29,11 +29,11 @@ - + - + - +
diff --git a/commonoptions/index.html b/commonoptions/index.html index 93ed27257..375d302b4 100644 --- a/commonoptions/index.html +++ b/commonoptions/index.html @@ -4,7 +4,7 @@ - + @@ -32,12 +32,12 @@ - + - + - - + +
diff --git a/development/index.html b/development/index.html index 14f21ba6e..571b391b2 100644 --- a/development/index.html +++ b/development/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + +
diff --git a/haplotagdata/index.html b/haplotagdata/index.html index 9f2d67c8a..a719bb5c4 100644 --- a/haplotagdata/index.html +++ b/haplotagdata/index.html @@ -4,7 +4,7 @@ - + @@ -34,11 +34,11 @@ - + - + - + diff --git a/index.html b/index.html index 0ba6b1301..604279c88 100644 --- a/index.html +++ b/index.html @@ -4,7 +4,7 @@ - + @@ -34,11 +34,11 @@ - + - + - +
diff --git a/install/index.html b/install/index.html index fe8ebf3ef..1b917eef3 100644 --- a/install/index.html +++ b/install/index.html @@ -4,7 +4,7 @@ - + @@ -32,12 +32,12 @@ - + - + - - + +
diff --git a/issues/index.html b/issues/index.html index f3be95633..7da8babb5 100644 --- a/issues/index.html +++ b/issues/index.html @@ -4,7 +4,7 @@ - + @@ -32,12 +32,12 @@ - + - + - - + +
diff --git a/modules/align/bwa/index.html b/modules/align/bwa/index.html index 258ea1b00..7f9dea871 100644 --- a/modules/align/bwa/index.html +++ b/modules/align/bwa/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + + diff --git a/modules/align/ema/index.html b/modules/align/ema/index.html index be6c052ca..a55299485 100644 --- a/modules/align/ema/index.html +++ b/modules/align/ema/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + + diff --git a/modules/align/index.html b/modules/align/index.html index 912d98c7c..c4064c092 100644 --- a/modules/align/index.html +++ b/modules/align/index.html @@ -4,7 +4,7 @@ - + @@ -32,11 +32,11 @@ - + - + - +
diff --git a/modules/align/strobe/index.html b/modules/align/strobe/index.html index b0a843858..38eff2c69 100644 --- a/modules/align/strobe/index.html +++ b/modules/align/strobe/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + + diff --git a/modules/deconvolve/index.html b/modules/deconvolve/index.html index 8565f9182..4e38e0107 100644 --- a/modules/deconvolve/index.html +++ b/modules/deconvolve/index.html @@ -4,7 +4,7 @@ - + @@ -32,12 +32,12 @@ - + - + - - + + @@ -265,7 +265,7 @@

.F .1 - or + _1 _R1_001 @@ -282,7 +282,7 @@

.R .2 - or + _2 _R2_001 diff --git a/modules/demultiplex/index.html b/modules/demultiplex/index.html index 23c0cbb18..b39533880 100644 --- a/modules/demultiplex/index.html +++ b/modules/demultiplex/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + + diff --git a/modules/impute/index.html b/modules/impute/index.html index 8af9aa27a..6e38b497b 100644 --- a/modules/impute/index.html +++ b/modules/impute/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + + diff --git a/modules/other/index.html b/modules/other/index.html index ff5e38773..7dcab1c12 100644 --- a/modules/other/index.html +++ b/modules/other/index.html @@ -4,7 +4,7 @@ - + @@ -32,12 +32,12 @@ - + - + - - + +
diff --git a/modules/phase/index.html b/modules/phase/index.html index 74b1e3253..653368cc8 100644 --- a/modules/phase/index.html +++ b/modules/phase/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + + diff --git a/modules/preflight/index.html b/modules/preflight/index.html index 383bc4717..5c55f3e62 100644 --- a/modules/preflight/index.html +++ b/modules/preflight/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + +
diff --git a/modules/qc/index.html b/modules/qc/index.html index bc8271d86..cac6e3198 100644 --- a/modules/qc/index.html +++ b/modules/qc/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + + diff --git a/modules/simulate/index.html b/modules/simulate/index.html index ac0112594..e6ebc2a90 100644 --- a/modules/simulate/index.html +++ b/modules/simulate/index.html @@ -4,7 +4,7 @@ - + @@ -32,11 +32,11 @@ - + - + - +
diff --git a/modules/simulate/simulate-linkedreads/index.html b/modules/simulate/simulate-linkedreads/index.html index 0f4b160e7..c695d9f49 100644 --- a/modules/simulate/simulate-linkedreads/index.html +++ b/modules/simulate/simulate-linkedreads/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + + diff --git a/modules/simulate/simulate-variants/index.html b/modules/simulate/simulate-variants/index.html index 35c834ce9..9143383e4 100644 --- a/modules/simulate/simulate-variants/index.html +++ b/modules/simulate/simulate-variants/index.html @@ -4,7 +4,7 @@ - + @@ -32,12 +32,12 @@ - + - + - - + + diff --git a/modules/snp/index.html b/modules/snp/index.html index d79f9f83c..a36a02fc5 100644 --- a/modules/snp/index.html +++ b/modules/snp/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + + diff --git a/modules/sv/index.html b/modules/sv/index.html index 972660255..425a13a94 100644 --- a/modules/sv/index.html +++ b/modules/sv/index.html @@ -4,7 +4,7 @@ - + @@ -32,11 +32,11 @@ - + - + - +
diff --git a/modules/sv/leviathan/index.html b/modules/sv/leviathan/index.html index 6c43b97d4..7af187715 100644 --- a/modules/sv/leviathan/index.html +++ b/modules/sv/leviathan/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + + diff --git a/modules/sv/naibr/index.html b/modules/sv/naibr/index.html index 45d99d846..87c06fbd7 100644 --- a/modules/sv/naibr/index.html +++ b/modules/sv/naibr/index.html @@ -4,7 +4,7 @@ - + @@ -34,12 +34,12 @@ - + - + - - + + diff --git a/resources/js/config.js b/resources/js/config.js index f83a740a8..736401a81 100644 --- a/resources/js/config.js +++ b/resources/js/config.js @@ -1 +1 @@ -var __DOCS_CONFIG__ = {"id":"o230Th7/nuDyYPk4VdPtp087wtvYNQs2II7","key":"mREHhGo9gZRhB/9HhBET3C5uqVn6qmElJY2sovImR9U.pSPSIdP+/271SASuwhBDOxjz8ZNRQsaY6GfcZw6c6cp9JWXDiL8p3bJvIKuDzMjKUMceZDyDNnLHUWhJCvt+iA.125","base":"/harpy/","host":"pdimens.github.io","version":"1.0.0","useRelativePaths":true,"documentName":"index.html","appendDocumentName":false,"trailingSlash":true,"preloadSearch":false,"cacheBustingToken":"3.5.0.773525426656","cacheBustingStrategy":"query","sidebarFilterPlaceholder":"Filter","toolbarFilterPlaceholder":"Filter","showSidebarFilter":true,"filterNotFoundMsg":"No member names found containing the query \"{query}\"","maxHistoryItems":15,"homeIcon":"","access":[{"value":"public","label":"Public"},{"value":"protected","label":"Protected"}],"toolbarLinks":[{"id":"fields","label":"Fields"},{"id":"properties","label":"Properties"},{"id":"methods","label":"Methods"},{"id":"events","label":"Events"}],"sidebar":[{"n":"/","l":"Home","s":""},{"n":"install","l":"Install","s":""},{"n":"modules","l":"Modules","c":false,"i":[{"n":"align","l":"Align","i":[{"n":"bwa","l":"BWA","s":""},{"n":"ema","l":"EMA","s":""},{"n":"strobe","l":"Strobe","s":""}],"s":""},{"n":"deconvolve","l":"Deconvolve","s":""},{"n":"demultiplex","l":"Demultiplex","s":""},{"n":"impute","l":"Impute","s":""},{"n":"other","l":"Other","s":""},{"n":"phase","l":"Phase","s":""},{"n":"preflight","l":"Preflight","s":""},{"n":"qc","l":"QC","s":""},{"n":"simulate","l":"Simulate","i":[{"n":"simulate-linkedreads","l":"Linked Reads","s":""},{"n":"simulate-variants","l":"Variants","s":""}],"s":""},{"n":"snp","l":"SNP","s":""},{"n":"sv","l":"SV","i":[{"n":"leviathan","l":"Leviathan","s":""},{"n":"naibr","l":"Naibr","s":""}],"s":""}],"s":""},{"n":"haplotagdata","l":"Haplotag data","s":""},{"n":"commonoptions","l":"Common Options","s":""},{"n":"issues","l":"Common Issues","s":""},{"n":"snakemake","l":"Snakemake things","s":""},{"n":"software","l":"Software","s":""},{"n":"development","l":"Development","s":""},{"n":"blog","l":"Blog","v":false,"i":[{"n":"softwareenvironments","l":" Choosing a software runtime method","v":false,"s":""},{"n":"filteringsnps","l":" Filtering Variants","v":false,"s":""}]}],"search":{"mode":1,"minChars":2,"maxResults":20,"placeholder":"Search","hotkeys":["k"],"noResultsFoundMsg":"Sorry, no results found.","recognizeLanguages":true,"languages":[0],"preload":false},"resources":{"History_Title_Label":"History","History_ClearLink_Label":"Clear","History_NoHistory_Label":"No history items","API_AccessFilter_Label":"Access","API_ParameterSection_Label":"PARAMETERS","API_SignatureSection_Label":"SIGNATURE","API_CopyHint_Label":"Copy","API_CopyNameHint_Label":"Copy name","API_CopyLinkHint_Label":"Copy link","API_CopiedAckHint_Label":"Copied!","API_MoreOverloads_Label":"more","API_MoreDropdownItems_Label":"More","API_OptionalParameter_Label":"optional","API_DefaultParameterValue_Label":"Default value","API_InheritedFilter_Label":"Inherited","Search_Input_Placeholder":"Search","Toc_Contents_Label":"Contents","Toc_RelatedClasses_Label":"Related Classes","History_JustNowTime_Label":"just now","History_AgoTime_Label":"ago","History_YearTime_Label":"y","History_MonthTime_Label":"mo","History_DayTime_Label":"d","History_HourTime_Label":"h","History_MinuteTime_Label":"m","History_SecondTime_Label":"s"}}; +var __DOCS_CONFIG__ = {"id":"d9+eGgCRwKYF4gFJ3Xgz230M7o9Wfn0aRgE","key":"WP5TDzA26kI0ZMEMDGn7wf6uH1ZFODzWqSG7YV6YM+U.sks/+3dTgcRkYDD9HcUzPnPvrT4yz/8BcXzrLEZdXqzDFhXHc948UwjI+DuTsliD03Nvm6UHRuLQk7+kaKn30A.68","base":"/harpy/","host":"pdimens.github.io","version":"1.0.0","useRelativePaths":true,"documentName":"index.html","appendDocumentName":false,"trailingSlash":true,"preloadSearch":false,"cacheBustingToken":"3.5.0.773761634790","cacheBustingStrategy":"query","sidebarFilterPlaceholder":"Filter","toolbarFilterPlaceholder":"Filter","showSidebarFilter":true,"filterNotFoundMsg":"No member names found containing the query \"{query}\"","maxHistoryItems":15,"homeIcon":"","access":[{"value":"public","label":"Public"},{"value":"protected","label":"Protected"}],"toolbarLinks":[{"id":"fields","label":"Fields"},{"id":"properties","label":"Properties"},{"id":"methods","label":"Methods"},{"id":"events","label":"Events"}],"sidebar":[{"n":"/","l":"Home","s":""},{"n":"install","l":"Install","s":""},{"n":"modules","l":"Modules","c":false,"i":[{"n":"align","l":"Align","i":[{"n":"bwa","l":"BWA","s":""},{"n":"ema","l":"EMA","s":""},{"n":"strobe","l":"Strobe","s":""}],"s":""},{"n":"deconvolve","l":"Deconvolve","s":""},{"n":"demultiplex","l":"Demultiplex","s":""},{"n":"impute","l":"Impute","s":""},{"n":"other","l":"Other","s":""},{"n":"phase","l":"Phase","s":""},{"n":"preflight","l":"Preflight","s":""},{"n":"qc","l":"QC","s":""},{"n":"simulate","l":"Simulate","i":[{"n":"simulate-linkedreads","l":"Linked Reads","s":""},{"n":"simulate-variants","l":"Variants","s":""}],"s":""},{"n":"snp","l":"SNP","s":""},{"n":"sv","l":"SV","i":[{"n":"leviathan","l":"Leviathan","s":""},{"n":"naibr","l":"Naibr","s":""}],"s":""}],"s":""},{"n":"haplotagdata","l":"Haplotag data","s":""},{"n":"commonoptions","l":"Common Options","s":""},{"n":"issues","l":"Common Issues","s":""},{"n":"snakemake","l":"Snakemake things","s":""},{"n":"software","l":"Software","s":""},{"n":"development","l":"Development","s":""},{"n":"blog","l":"Blog","v":false,"i":[{"n":"softwareenvironments","l":" Choosing a software runtime method","v":false,"s":""},{"n":"filteringsnps","l":" Filtering Variants","v":false,"s":""}]}],"search":{"mode":1,"minChars":2,"maxResults":20,"placeholder":"Search","hotkeys":["k"],"noResultsFoundMsg":"Sorry, no results found.","recognizeLanguages":true,"languages":[0],"preload":false},"resources":{"History_Title_Label":"History","History_ClearLink_Label":"Clear","History_NoHistory_Label":"No history items","API_AccessFilter_Label":"Access","API_ParameterSection_Label":"PARAMETERS","API_SignatureSection_Label":"SIGNATURE","API_CopyHint_Label":"Copy","API_CopyNameHint_Label":"Copy name","API_CopyLinkHint_Label":"Copy link","API_CopiedAckHint_Label":"Copied!","API_MoreOverloads_Label":"more","API_MoreDropdownItems_Label":"More","API_OptionalParameter_Label":"optional","API_DefaultParameterValue_Label":"Default value","API_InheritedFilter_Label":"Inherited","Search_Input_Placeholder":"Search","Toc_Contents_Label":"Contents","Toc_RelatedClasses_Label":"Related Classes","History_JustNowTime_Label":"just now","History_AgoTime_Label":"ago","History_YearTime_Label":"y","History_MonthTime_Label":"mo","History_DayTime_Label":"d","History_HourTime_Label":"h","History_MinuteTime_Label":"m","History_SecondTime_Label":"s"}}; diff --git a/sitemap.xml.gz b/sitemap.xml.gz index 38329731bdb8db71ed689bc8bf96ff3caff09257..b80917de316057f1cbe67b0aabe72c42cdf58533 100644 GIT binary patch literal 566 zcmV-60?GX!iwFP!000001I(DolG`8U6Q9+GFG;9mA3UR`TX)}vPzzd(Y6bQ z6py2@rCri6`;8F8Fr=hewbE1SLM^Cl;sc4>OOd7Pq zZRX2O_Vgvn-A1pnK4=#-zZUV2x8nQL89>|!{*h#FT>U)>n@WXx6rCr{Eb+Dc4fpM&$~HBH4m2Z5Vm;40NC>f|8nf5A>c6Oi4(=3@PTe?cydY^oG`aF9`9*fDY z3x*U=qp+oY(lGn25W_H}q*=AnQ|dx3sBB_~#Py-b(mc7$*`6A1&8wNi@;qmr=eanK zCdFhr9p5yz@y@ui809HW@Re?rrL@-Ebca+s(a7Lm#7>M-S9wX?x~f=Yi`6XK%(C^< zBHPa6m4A(L*U^it584IIFGc*~o%qok0mPNyA4v|z)$hYuZ2pcDHMYj^l&)=^b)KVP z>HqbVrJEH7tdZV0mUSgrBDg+*xU?mf#z2r37^Jv(XA}u(bZsGESgvm+0&1OOsdVc* zRuD3{bXM1OQjGuy16H%ui>RN$gtqLNMM^yzS zD~v)x4qZmJI<69#>rPkiEmYqA4Khdl2Kfnxp!##Qd2UE?G5HPv0RR6305(TdXHXLW E00{yQEdT%j diff --git a/snakemake/index.html b/snakemake/index.html index 77adb559e..5889b08e6 100644 --- a/snakemake/index.html +++ b/snakemake/index.html @@ -4,7 +4,7 @@ - + @@ -32,12 +32,12 @@ - + - + - - + +
diff --git a/software/index.html b/software/index.html index 894d9bf71..af974f0c7 100644 --- a/software/index.html +++ b/software/index.html @@ -4,7 +4,7 @@ - + @@ -32,11 +32,11 @@ - + - + - +