/* Illumina library structure color scheme */
/* Based on https://teichlab.github.io/scg_lib_structs/ */

seq {
    font-family: 'Courier New', 'Fira Mono', monospace;
    font-size: 0.9em;
}

/* DNA sequence element colors */
p5 {color: #08519c;}      /* Illumina P5 adaptor - dark blue */
p7 {color: #a50f15;}      /* Illumina P7 adaptor - dark red */
s5 {color: #6baed6;}      /* Truseq Read 1 / i5 related - light blue */
s7 {color: #fc9272;}      /* Truseq Read 2 / i7 related - light salmon */
r1 {color: #4a1486;}      /* Nextera Read 1 - dark purple */
r2 {color: #6a51a3;}      /* Nextera Read 2 - purple */
t7 {color: blue;}         /* i7 index (NNNN) - blue */
cbc {color: #f768a1;}     /* Cell barcode - pink */
umi {color: #807dba;}     /* UMI - light purple */
me {color: #969696;}      /* Insert/methylation - gray */
tso {color: #2ca25f;}     /* TSO - green */

/* Sequencing primers */
pe1 {color: #bcbddc;}
pe2 {color: #9ebcda;}

/* Additional elements */
w1 {color: #f03b20;}      /* Warning/highlight - orange-red */
nexus {color: #f0b7a6;}
bulge {color: #f3b44e;}

/* Custom formatting for code blocks with seq class */
pre.seq {
    background-color: #f8f9fa;
    padding: 1em;
    border-radius: 4px;
    line-height: 1.6;
    overflow-x: auto;
    width: max-content;  /* Auto-size to content width */
    max-width: 100vw;  /* Don't exceed viewport width */
    /* width: 200%; Wider than default container */
    /* margin-left: -10%;  Center the wider box */

    
}

/* Make sure custom tags display as inline */
p5, p7, s5, s7, r1, r2, t7, cbc, umi, me, tso, pe1, pe2, w1, nexus, bulge {
    display: inline;
    font-weight: normal;
}