fgumi 0.2.0

High-performance tools for UMI-tagged sequencing data: extraction, grouping, and consensus calling
Documentation 
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/* ============================================================
   Fulcrum Genomics — fgumi documentation theme
   "Lab Readout": clinical precision, bold genomics energy
   ============================================================ */

/* --- Google Fonts: IBM Plex family -------------------------- */
@import 'https://fonts.googleapis.com/css2?family=IBM+Plex+Mono:ital,wght@0,400;0,600;1,400&family=IBM+Plex+Sans:ital,wght@0,300;0,400;0,600;0,700;1,400&family=IBM+Plex+Serif:wght@400;600&display=swap';

/* --- Fulcrum Genomics brand palette ------------------------- */
:root {
    --fg-blue:       #26a8e0;
    --fg-green:      #38b44a;
    --fg-pacific:    #1693b9;
    --fg-sky:        #4dcce8;
    --fg-teal:       #2fae99;
    --fg-emerald:    #4dcc68;
    --fg-forest:     #269e2a;
    --fg-deep-blue:  #160052;
    --fg-night-blue: #10003d;
    --fg-ghost:      #f8f5ff;
    --fg-gray:       #a5a8a7;
}

/* --- Body typography ---------------------------------------- */

/* Override mdBook's small root font size */
html {
    font-size: 18px !important;
    scroll-behavior: smooth;
}

body {
    font-family: 'IBM Plex Sans', sans-serif !important;
    font-size: 1rem !important;
    line-height: 1.75 !important;
}

code, kbd, pre, samp, .hljs {
    font-family: 'IBM Plex Mono', monospace !important;
}

h1, h2, h3, h4, h5, h6 {
    font-family: 'IBM Plex Sans', sans-serif !important;
    font-weight: 600;
    letter-spacing: -0.01em;
    line-height: 1.3;
}

.content main {
    font-size: 1rem !important;
    line-height: 1.8 !important;
}

.content main p,
.content main li,
.content main td,
.content main th {
    font-size: 1rem !important;
    line-height: 1.8 !important;
}

.content main h1 { font-size: 2.1rem !important;  margin-top: 1rem !important; }
.content main h2 { font-size: 1.55rem !important; margin-top: 2rem !important; margin-bottom: 1rem !important; }
.content main h3 { font-size: 1.25rem !important; margin-top: 1.5rem !important; }
.content main h4 { font-size: 1.15rem !important; color: var(--fg-pacific); }
.content main h5 { font-size: 1rem !important; color: var(--fg-pacific); }
.content main h6 { font-size: 0.9rem !important; color: var(--fg-pacific); }

/* ============================================================
   NAVY THEME (default dark)
   ============================================================ */
.navy {
    --bg:                   #fafbff;
    --fg:                   #1a1a2e;
    --sidebar-bg:           transparent;   /* handled by gradient */
    --sidebar-fg:           #e2e8f0;
    --sidebar-active:       #ffffff;
    --sidebar-spacer:       rgba(255,255,255,0.08);
    --scrollbar:            rgba(255,255,255,0.2);
    --icons:                rgba(255,255,255,0.5);
    --icons-hover:          var(--fg-sky);
    --links:                var(--fg-blue);
    --inline-code-color:    var(--fg-deep-blue);
    --theme-popup-bg:       #ffffff;
    --theme-popup-border:   #e0e0f0;
    --theme-hover:          var(--fg-ghost);
    --quote-bg:             #e8f6ed;
    --quote-border:         var(--fg-green);
    --warning-border:       var(--fg-blue);
    --table-border-color:   #e0e4f0;
    --table-header-bg:      #eef6ff;
    --table-alternate-bg:   #f0f8ff;
    --searchbar-border-color: var(--fg-blue);
    --searchbar-bg:         #ffffff;
    --searchbar-fg:         var(--fg-deep-blue);
    --searchbar-shadow-color: rgba(38,168,224,0.3);
    --searchresults-header-fg: var(--fg-gray);
    --searchresults-border-color: #e0e0f0;
    --searchresults-li-bg:  var(--fg-ghost);
    --search-mark-bg:       var(--fg-teal);
}

/* --- Content area: light, clean ----------------------------- */
.navy .content main,
.navy .page-wrapper {
    background: #fafbff;
    color: #1a1a2e;
}

/* ============================================================
   LIGHT THEME
   ============================================================ */
.light {
    --bg:                   #ffffff;
    --fg:                   #1a1a2e;
    --sidebar-bg:           transparent;
    --sidebar-fg:           #e2e8f0;
    --sidebar-active:       #ffffff;
    --sidebar-spacer:       rgba(255,255,255,0.08);
    --scrollbar:            rgba(255,255,255,0.2);
    --icons:                rgba(255,255,255,0.5);
    --icons-hover:          var(--fg-sky);
    --links:                var(--fg-blue);
    --inline-code-color:    var(--fg-deep-blue);
    --theme-popup-bg:       #ffffff;
    --theme-popup-border:   #e0e0f0;
    --theme-hover:          var(--fg-ghost);
    --quote-bg:             #e8f6ed;
    --quote-border:         var(--fg-green);
    --warning-border:       var(--fg-blue);
    --table-border-color:   #e0e4f0;
    --table-header-bg:      #eef6ff;
    --table-alternate-bg:   #f0f8ff;
    --searchbar-border-color: var(--fg-blue);
    --searchbar-bg:         #ffffff;
    --searchbar-fg:         var(--fg-deep-blue);
    --searchbar-shadow-color: rgba(38,168,224,0.3);
    --searchresults-header-fg: var(--fg-gray);
    --searchresults-border-color: #e0e0f0;
    --searchresults-li-bg:  var(--fg-ghost);
    --search-mark-bg:       var(--fg-teal);
}

/* ============================================================
   SIDEBAR — FG Night Blue ➜ Forest Green gradient
   ============================================================ */
.sidebar {
    background: linear-gradient(
        160deg,
        #10003d 0%,
        #160052 35%,
        #0d2e1a 75%,
        #0a2214 100%
    ) !important;
    border-right: 1px solid rgba(56, 180, 74, 0.2);
}

.sidebar .sidebar-scrollbox {
    padding-top: 0.5rem;
}

/* Sidebar book title */
.sidebar .sidebar-scrollbox .sidebar-title {
    font-family: 'IBM Plex Sans', sans-serif !important;
    font-weight: 700;
    font-size: 1.1rem;
    color: #ffffff;
    letter-spacing: 0.02em;
    padding: 0.75rem 1rem 0.5rem;
    display: block;
}

/* All sidebar links */
.sidebar a {
    color: rgba(226, 232, 240, 0.95) !important;
    font-size: 0.875rem;
    transition: color 0.15s ease, padding-left 0.15s ease;
}

.sidebar a:hover {
    color: var(--fg-sky) !important;
    text-decoration: none;
}

/* Section header spans (no-link items like "Core Concepts") */
.sidebar .chapter-link-wrapper > span {
    color: var(--fg-blue) !important;
    font-size: 0.8rem;
    font-weight: 500;
}

/* Active page — green left-bar accent */
.sidebar a.active {
    color: #ffffff !important;
    position: relative;
    font-weight: 600;
}

.sidebar a.active::before {
    content: '';
    position: absolute;
    left: 0;
    top: 0;
    bottom: 0;
    width: 3px;
    background: var(--fg-green);
    border-radius: 0 2px 2px 0;
}

/* Top-level part titles (User Guide, Tool Reference, Metrics Reference) */
.sidebar-scrollbox .part-title {
    color: var(--fg-emerald) !important;
    font-size: 0.8rem !important;
    font-family: 'IBM Plex Sans', sans-serif !important;
    text-transform: uppercase;
    letter-spacing: 0.1em;
    font-weight: 700;
    margin-top: 1.5rem;
    padding-left: 0 !important;
}

/* Sidebar separator lines */
.sidebar hr {
    border-color: rgba(56, 180, 74, 0.2);
    margin: 0.5rem 1rem;
}

/* ============================================================
   TOP MENU BAR
   ============================================================ */
.menu-bar,
.menu-bar .menu-bar-sticky-container {
    background: var(--fg-night-blue) !important;
    border-bottom: 2px solid var(--fg-green) !important;
}

.menu-title {
    font-family: 'IBM Plex Sans', sans-serif !important;
    font-weight: 600 !important;
    letter-spacing: -0.01em !important;
}

.menu-bar i.fa,
.menu-bar .icon-button {
    color: rgba(255,255,255,0.75) !important;
}

.menu-bar i.fa:hover,
.menu-bar .icon-button:hover {
    color: var(--fg-sky) !important;
}

/* ============================================================
   CONTENT AREA
   ============================================================ */

/* H1: green underline */
.content main h1 {
    color: var(--fg-deep-blue);
    border-bottom: 3px solid var(--fg-green);
    padding-bottom: 0.4rem;
    margin-bottom: 1.5rem;
}

.content main h2 {
    color: var(--fg-deep-blue);
    border-bottom: 1px solid #e0e4f0;
    padding-bottom: 0.25rem;
}

.content main h3 {
    color: var(--fg-pacific);
}

/* Links — FG Blue for visibility, Sky on hover */
a {
    color: var(--fg-blue);
    text-decoration: none;
}

a:hover {
    color: var(--fg-sky);
    text-decoration: underline;
}

/* ============================================================
   BREADCRUMBS
   ============================================================ */
.fg-breadcrumb {
    font-family: 'IBM Plex Mono', monospace;
    font-size: 0.8rem;
    color: var(--fg-gray);
    margin-bottom: 1.5rem;
    display: flex;
    align-items: center;
    flex-wrap: wrap;
    gap: 0.25rem;
}

.fg-breadcrumb a {
    color: var(--fg-pacific) !important;
    text-decoration: none;
}

.fg-breadcrumb a:hover {
    color: var(--fg-blue) !important;
    text-decoration: underline;
}

.fg-breadcrumb-sep {
    color: var(--fg-gray);
    margin: 0 0.1rem;
    opacity: 0.6;
}

.fg-breadcrumb-current {
    color: var(--fg);
    font-weight: 600;
}

/* ============================================================
   CODE
   ============================================================ */

/* Inline code — high specificity to beat mdBook's theme overrides */
.content main code,
.content p code,
.content li code,
.content td code,
.content th code,
.content h1 code,
.content h2 code,
.content h3 code,
.content h4 code,
p code,
li code,
td code {
    font-family: 'IBM Plex Mono', monospace !important;
    background: #dff0fb !important;
    color: #0d2d52 !important;
    border: 1px solid #b3d9f0 !important;
    border-radius: 3px !important;
    padding: 0.1em 0.4em !important;
    font-size: 0.9em !important;
}

/* Code blocks — green left accent */
pre {
    border-left: 4px solid var(--fg-green) !important;
    border-radius: 0 6px 6px 0 !important;
    background: #f4f8ff !important;
    box-shadow: inset 0 1px 3px rgba(22, 0, 82, 0.06);
    padding: 0.75rem 1rem !important;
}

pre code {
    background: transparent;
    border: none;
    padding: 0;
    color: #1a1a2e;
    font-size: 0.875rem;
    line-height: 1.6;
}

/* Copy button */
.copy-button {
    border: 1px solid var(--fg-green) !important;
    color: var(--fg-forest) !important;
    background: rgba(56, 180, 74, 0.2) !important;
}

.copy-button:hover {
    background: rgba(56, 180, 74, 0.35) !important;
}

/* ============================================================
   TABLES
   ============================================================ */
table {
    width: 100%;
    border-collapse: collapse;
    margin: 1.25rem 0;
    font-size: 0.9rem;
    box-shadow: 0 1px 4px rgba(22, 0, 82, 0.07);
    border-radius: 6px;
    overflow: hidden;
}

table th {
    background: var(--fg-deep-blue);
    color: #ffffff;
    text-align: left;
    padding: 0.6rem 0.85rem;
    font-family: 'IBM Plex Mono', monospace;
    font-size: 0.8rem;
    letter-spacing: 0.05em;
    text-transform: uppercase;
    font-weight: 600;
}

table td {
    padding: 0.55rem 0.85rem;
    border-bottom: 1px solid var(--table-border-color);
    vertical-align: top;
}

table tr:last-child td {
    border-bottom: none;
}

table tr:nth-child(even) td {
    background: #f0f8ff;
}

table tr:hover td {
    background: #d6ebff;
}

/* ============================================================
   BLOCKQUOTES — green accent (notes, tips)
   ============================================================ */
blockquote {
    border-left: 4px solid var(--fg-green) !important;
    background: #e8f6ed !important;
    padding: 0.85rem 1.1rem !important;
    border-radius: 0 6px 6px 0;
    color: #1a3a28;
    margin: 1.25rem 0;
}

blockquote p {
    margin: 0;
}

blockquote strong {
    color: var(--fg-forest);
}

/* ============================================================
   SEARCH
   ============================================================ */
#searchbar {
    font-family: 'IBM Plex Mono', monospace !important;
    border: 1px solid var(--fg-blue);
    border-radius: 4px;
    font-size: 0.875rem;
}

#searchbar:focus {
    border-color: var(--fg-green);
    box-shadow: 0 0 0 3px rgba(56, 180, 74, 0.5);
    outline: 2px solid transparent;
}

/* ============================================================
   TOOL REFERENCE (auto-generated pages)
   ============================================================ */

/* Category labels */
.tool-category {
    font-family: 'IBM Plex Mono', monospace;
    font-weight: 600;
    color: var(--fg-green);
    margin-top: 2rem;
    margin-bottom: 0.5rem;
    font-size: 0.75rem;
    text-transform: uppercase;
    letter-spacing: 0.1em;
    border-bottom: 1px solid rgba(56, 180, 74, 0.3);
    padding-bottom: 0.3rem;
}

.tool-description code,
.metric-description code {
    font-size: 0.875em;
}

/* ============================================================
   LANDING PAGE
   ============================================================ */
.hero {
    text-align: center;
    padding: 3rem 0 2rem;
    margin-bottom: 3rem;
    border-bottom: 1px solid #e0e4f0;
}

.hero h1 {
    font-size: 3rem;
    font-weight: 700;
    color: var(--fg-deep-blue);
    border-bottom: none;
    margin-bottom: 0.5rem;
    letter-spacing: -0.03em;
}

.hero h1 span {
    color: var(--fg-green);
}

.hero .tagline {
    font-size: 1.15rem;
    color: var(--fg-pacific);
    font-weight: 300;
}

/* Feature / use-case cards */
.use-cards {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(240px, 1fr));
    gap: clamp(1rem, 3vw, 1.5rem);
    margin: 1.5rem 0;
}

.use-card {
    border: 1px solid #e0e4f0;
    border-top: 4px solid var(--fg-blue);
    border-radius: 0 0 8px 8px;
    padding: 1.5rem;
    background: #fafbff;
    box-shadow: 0 2px 8px rgba(22, 0, 82, 0.06);
    transition: box-shadow 0.2s ease, transform 0.2s ease;
}

.use-card:hover {
    box-shadow: 0 4px 16px rgba(22, 0, 82, 0.12);
    transform: translateY(-2px);
}

.use-card:nth-child(2) { border-top-color: var(--fg-green); }
.use-card:nth-child(3) { border-top-color: var(--fg-teal); }
.use-card:nth-child(4) { border-top-color: var(--fg-pacific); }

.use-card h3 {
    margin-top: 0;
    color: var(--fg-deep-blue);
    font-size: 1rem;
}

/* ============================================================
   FG BRANDING INJECTED BY sidebar-brand.js
   ============================================================ */
.fg-brand-header {
    padding: 1.1rem 1rem 0.85rem;
    border-bottom: 1px solid rgba(56, 180, 74, 0.25);
    margin-bottom: 0.5rem;
    display: flex;
    flex-direction: column;
    gap: 0.4rem;
}

.fg-brand-link {
    display: block;
    line-height: 0;
}

.fg-brand-logo {
    height: 64px;
    width: auto;
    display: block;
    opacity: 0.92;
    transition: opacity 0.15s ease;
}

.fg-brand-link:hover .fg-brand-logo {
    opacity: 1;
}

.fg-brand-divider {
    height: 1px;
    background: rgba(56, 180, 74, 0.2);
    margin: 0.1rem 0;
}

.fg-brand-product {
    font-family: 'IBM Plex Sans', sans-serif;
    font-weight: 700;
    font-size: 1.2rem;
    letter-spacing: 0.01em;
    padding: 0 0.1rem;
    line-height: 1.2;
}

.fg-brand-tagline {
    font-family: 'IBM Plex Mono', monospace;
    font-size: 0.7rem;
    color: rgba(255, 255, 255, 0.5);
    letter-spacing: 0.05em;
    padding: 0 0.1rem;
}

.fg-brand-corp {
    font-family: 'IBM Plex Sans', sans-serif;
    font-size: 0.72rem;
    color: rgba(77, 204, 104, 0.7) !important;
    text-decoration: none !important;
    letter-spacing: 0.02em;
    margin-top: 0.15rem;
    transition: color 0.15s ease;
}

.fg-brand-corp:hover {
    color: var(--fg-emerald) !important;
    text-decoration: none !important;
}

/* ============================================================
   CONTENT WIDTH & MARGINS
   ============================================================ */

/* Override mdBook's narrow 750px content column */
:root {
    --content-max-width: 98%;
    --page-padding: 10px;
}

.content {
    padding: 0 0.75rem 50px !important;
}

@media (min-width: 768px) {
    .content {
        padding: 0 1.5rem 50px !important;
    }
}

.content main {
    max-width: 1000px !important;
    margin-inline-start: 0 !important;
    margin-inline-end: auto !important;
}

.page-wrapper {
    padding-bottom: 3rem;
}

@media (min-width: 1400px) {
    .content main {
        max-width: 1200px !important;
    }
}

/* ============================================================
   BYLINE (inline attribution next to h1 on index page)
   ============================================================ */
.fg-byline-inline {
    font-size: 0.7rem;
    font-weight: 400;
    color: rgba(255, 255, 255, 0.55);
    vertical-align: middle;
    margin-left: 0.6em;
    white-space: nowrap;
}

.fg-byline-inline a {
    color: rgba(255, 255, 255, 0.55);
    text-decoration: none;
}

.fg-byline-inline a:hover {
    color: rgba(255, 255, 255, 0.9);
    text-decoration: none;
}

/* ============================================================
   VISIT US SECTION (index.md top + footer on all pages)
   ============================================================ */
.fg-visit-us {
    margin-top: 2.5rem;
    padding: 1.5rem 1rem 1.25rem;
    border: 1px solid var(--table-border-color);
    border-top: 4px solid var(--fg-green);
    border-radius: 0 0 8px 8px;
    background: var(--fg-ghost);
    text-align: center;
}

.fg-visit-us img {
    margin: 0 auto 1rem;
    display: block;
    max-width: 320px;
    width: 100%;
    height: auto;
}

.fg-visit-us p {
    font-size: 1rem;
    color: var(--fg);
    margin: 0 auto 1.25rem;
    max-width: 100%;
    text-align: center;
}

.fg-visit-buttons {
    display: flex;
    gap: 0.75rem;
    justify-content: center;
    flex-wrap: wrap;
    margin-bottom: 1rem;
}

.fg-btn {
    display: inline-flex;
    align-items: center;
    gap: 0.4rem;
    padding: 0.65rem 1.6rem;
    border-radius: 5px;
    font-family: 'IBM Plex Sans', sans-serif;
    font-weight: 600;
    font-size: 0.9rem;
    text-decoration: none !important;
    transition: filter 0.15s ease, transform 0.15s ease;
    letter-spacing: 0.02em;
}

.fg-btn:hover {
    filter: brightness(1.12);
    transform: translateY(-1px);
    text-decoration: none !important;
}

.fg-btn-green {
    background: var(--fg-green);
    color: #ffffff !important;
}

.fg-btn-blue {
    background: var(--fg-blue);
    color: #ffffff !important;
}

/* Quick links row in footer */
.fg-footer-links {
    display: flex;
    gap: 0.5rem;
    justify-content: center;
    flex-wrap: wrap;
    align-items: center;
    font-size: 0.85rem;
    margin-top: 0.75rem;
    padding-top: 0.75rem;
    border-top: 1px solid var(--table-border-color);
}

.fg-footer-links a {
    color: var(--fg-pacific) !important;
    text-decoration: none;
}

.fg-footer-links a:hover {
    color: var(--fg-blue) !important;
    text-decoration: underline;
}

.fg-footer-links .fg-footer-sep {
    color: var(--fg-gray);
    opacity: 0.5;
}

/* ============================================================
   MISC POLISH
   ============================================================ */

/* Better list spacing in content */
.content main li {
    margin-bottom: 0.25rem;
}

/* Warning/note callouts */
.warning {
    border-left: 4px solid var(--fg-blue) !important;
    background: #eef6ff !important;
}

/* ============================================================
   PRINT
   ============================================================ */
@media print {
    .sidebar,
    .menu-bar,
    .nav-chapters,
    .fg-breadcrumb,
    .fg-page-footer,
    .fg-visit-us {
        display: none !important;
    }
    .page-wrapper {
        margin-left: 0 !important;
    }
    .content main {
        max-width: 100% !important;
    }
}