diff --git a/COPYRIGHT b/COPYRIGHT index 179f708..74213e2 100644 --- a/COPYRIGHT +++ b/COPYRIGHT @@ -239,3 +239,8 @@ Incorporated in the United States and/or other countries. Font Awesome was made by Dave Gandy, for which we thank him. It truly is awesome. + +The export of the web viewer plots uses code from +https://stackoverflow.com/a/44769098, which according to the Stack +Overflow terms of service is licensed under CC BY-SA 3.0 +(https://creativecommons.org/licenses/by-sa/3.0/). diff --git a/Makefile b/Makefile index 0c4616b..9dad0ec 100644 --- a/Makefile +++ b/Makefile @@ -2,14 +2,14 @@ # VARIABLES # -VERSION = 0.9.2 +VERSION = 0.9.3 # # PATHS # SRC_DIR = src -CPP_DIR = $(shell readlink -f $(SRC_DIR)/cpp) +CPP_DIR = $(shell realpath -e $(SRC_DIR)/cpp) SCRIPTS_DIR = $(SRC_DIR)/scripts WEB_DIR = $(SRC_DIR)/web BUILD_DIR = build diff --git a/debian/changelog b/debian/changelog index 47f43a9..285b7b6 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +ataqv (0.9.3-1) unstable; urgency=low + + * Only consider autosomal alignments for peak duplicate metrics + * Add plot export to SVG and PNG (Firefox and Chrome only so far) + + -- Parker Lab Software Thu, 29 Jun 2017 10:00:00 -0500 + ataqv (0.9.2-1) unstable; urgency=low * Peak duplicate metrics; correct maximum fragment length measurement. diff --git a/docs/demo/css/ataqv.css b/docs/demo/css/ataqv.css index 14cfa41..0e99dde 100644 --- a/docs/demo/css/ataqv.css +++ b/docs/demo/css/ataqv.css @@ -450,6 +450,7 @@ table.dataTable thead th.sorting_desc::after { .tableContainer { margin-bottom: 2em; + min-width: 100em; } /* end tables */ @@ -493,7 +494,7 @@ table.dataTable thead th.sorting_desc::after { .tabs .active a { color: #fff; - border-bottom: 10px solid #444; + border-bottom: 4px solid #fff; } .tabs li:hover { @@ -537,16 +538,13 @@ table.dataTable thead th.sorting_desc::after { position: absolute; left: 0; top: 150%; - min-width: 20em; - max-width: 100%; + min-width: 30em; min-height: 2em; - max-height: 20em; display: block; content: attr(data-hovertext); text-align: left; font-size: 0.9em; font-weight: normal; - font-style: italic; white-space: normal; padding: 0.5em; color: #444; @@ -564,6 +562,10 @@ td:last-child *[data-hovertext]:hover::after, } #banner { + position: fixed; + top: 0; + z-index: 99999; + width: 100%; padding: 1.5em 0.5em 0 0.5em; background: #000; color: #fff; @@ -597,6 +599,10 @@ td:last-child *[data-hovertext]:hover::after, text-decoration: none; } +#exportCanvas { + display: none; +} + #mask { position: fixed; z-index: 999; @@ -615,7 +621,7 @@ td:last-child *[data-hovertext]:hover::after, display: none; opacity: 0; position: absolute; - max-width: 400px; + max-width: 600px; border: none; border-radius: 0.5rem; background: #fff; @@ -661,7 +667,7 @@ td:last-child *[data-hovertext]:hover::after, top: 0; z-index: 99999; left: -99999em; - height: 100%; + height: 100vh; width: 100%; padding: 10%; text-align: center; @@ -710,6 +716,12 @@ td:last-child *[data-hovertext]:hover::after, justify-content: flex-start; } +#sampleCount { + font-size: .75em; + opacity: 0.75; + padding-left: .5em; +} + #plotSampleList { margin: 0 0 1em 0; } @@ -818,10 +830,6 @@ td:last-child *[data-hovertext]:hover::after, fill: #eee; } -.axis.x .tick text { - transform: translate(-0.5em, 1em) rotate(-45deg); -} - .plotItem { opacity: 0.75; } @@ -835,6 +843,10 @@ td:last-child *[data-hovertext]:hover::after, opacity: 1; } +.legendItem.highlight { + color: rgba(255, 255, 0, 1) !important; +} + .dot.highlight { fill: rgba(255, 255, 0, 1) !important; } @@ -906,8 +918,8 @@ td:last-child *[data-hovertext]:hover::after, margin: 0 1em 0 2em; position: relative; font-size: 0.75rem; - height: 100p%; - overflow: auto; + max-height: 8em; + overflow-y: auto; user-select: none; -moz-user-select: none; -webkit-user-select: none; diff --git a/docs/demo/data/SRR891268___1.json.gz b/docs/demo/data/SRR891268___1.json.gz index edf51d9..1fa3801 100644 Binary files a/docs/demo/data/SRR891268___1.json.gz and b/docs/demo/data/SRR891268___1.json.gz differ diff --git a/docs/demo/data/SRR891269___1.json.gz b/docs/demo/data/SRR891269___1.json.gz index a61abab..f3008d6 100644 Binary files a/docs/demo/data/SRR891269___1.json.gz and b/docs/demo/data/SRR891269___1.json.gz differ diff --git a/docs/demo/data/SRR891270___1.json.gz b/docs/demo/data/SRR891270___1.json.gz index c178d11..6a31a2b 100644 Binary files a/docs/demo/data/SRR891270___1.json.gz and b/docs/demo/data/SRR891270___1.json.gz differ diff --git a/docs/demo/data/SRR891271___1.json.gz b/docs/demo/data/SRR891271___1.json.gz index 1f4d124..93cf761 100644 Binary files a/docs/demo/data/SRR891271___1.json.gz and b/docs/demo/data/SRR891271___1.json.gz differ diff --git a/docs/demo/data/SRR891272___1.json.gz b/docs/demo/data/SRR891272___1.json.gz index ba6a11f..3d15867 100644 Binary files a/docs/demo/data/SRR891272___1.json.gz and b/docs/demo/data/SRR891272___1.json.gz differ diff --git a/docs/demo/data/SRR891273___1.json.gz b/docs/demo/data/SRR891273___1.json.gz index d22bbb1..84da7b0 100644 Binary files a/docs/demo/data/SRR891273___1.json.gz and b/docs/demo/data/SRR891273___1.json.gz differ diff --git a/docs/demo/data/SRR891274___1.json.gz b/docs/demo/data/SRR891274___1.json.gz index ed4572b..e46861b 100644 Binary files a/docs/demo/data/SRR891274___1.json.gz and b/docs/demo/data/SRR891274___1.json.gz differ diff --git a/docs/demo/data/SRR891275___1.json.gz b/docs/demo/data/SRR891275___1.json.gz index 9094f7d..13a7722 100644 Binary files a/docs/demo/data/SRR891275___1.json.gz and b/docs/demo/data/SRR891275___1.json.gz differ diff --git a/docs/demo/data/SRR891276___1.json.gz b/docs/demo/data/SRR891276___1.json.gz index 034a292..b5bf855 100644 Binary files a/docs/demo/data/SRR891276___1.json.gz and b/docs/demo/data/SRR891276___1.json.gz differ diff --git a/docs/demo/data/SRR891277___1.json.gz b/docs/demo/data/SRR891277___1.json.gz index 4113e54..771ec3c 100644 Binary files a/docs/demo/data/SRR891277___1.json.gz and b/docs/demo/data/SRR891277___1.json.gz differ diff --git a/docs/demo/data/SRR891278___1.json.gz b/docs/demo/data/SRR891278___1.json.gz index e916906..1ae4837 100644 Binary files a/docs/demo/data/SRR891278___1.json.gz and b/docs/demo/data/SRR891278___1.json.gz differ diff --git a/docs/demo/data/SRR891279___1.json.gz b/docs/demo/data/SRR891279___1.json.gz index b0cf6c9..ae9645b 100644 Binary files a/docs/demo/data/SRR891279___1.json.gz and b/docs/demo/data/SRR891279___1.json.gz differ diff --git a/docs/demo/data/SRR891280___1.json.gz b/docs/demo/data/SRR891280___1.json.gz index 09c6ce3..eaac6fa 100644 Binary files a/docs/demo/data/SRR891280___1.json.gz and b/docs/demo/data/SRR891280___1.json.gz differ diff --git a/docs/demo/index.html b/docs/demo/index.html index 10abf99..2eaf231 100644 --- a/docs/demo/index.html +++ b/docs/demo/index.html @@ -12,6 +12,7 @@ + @@ -65,7 +66,7 @@

-

Samples

+

Samples

@@ -89,12 +90,14 @@

Plot help: HQAA fragment length distribution (FLD)

+ +
@@ -139,6 +142,8 @@

Plot help: distance from reference FLD

+ +
@@ -176,6 +181,8 @@

Plot help: TSS enrichment + + @@ -204,6 +211,8 @@

Plot help: Cumulative fraction of HQAA in peaks + + @@ -235,6 +244,8 @@

Plot help: Cumulative fraction of peak territory + + @@ -263,6 +274,8 @@

Plot help: Mapping quality distribution + + @@ -276,7 +289,7 @@

Plot help: Mapping quality distribution @@ -89,12 +90,14 @@

Plot help: HQAA fragment length distribution (FLD) + + @@ -139,6 +142,8 @@

Plot help: distance from reference FLD + + @@ -176,6 +181,8 @@

Plot help: TSS enrichment + + @@ -204,6 +211,8 @@

Plot help: Cumulative fraction of HQAA in peaks + + @@ -235,6 +244,8 @@

Plot help: Cumulative fraction of peak territory + + @@ -263,6 +274,8 @@

Plot help: Mapping quality distribution + + @@ -276,7 +289,7 @@

Plot help: Mapping quality distribution