=============
  Biocolor
=============

Open this file in VS Code with the extension active.

----------------------------------------------------------------
1.  Nucleotide auto-detect
----------------------------------------------------------------

Runs of 12+ nt at >=90% NT alphabet are auto-coloured:

    ACGTACGTACGTACGTACGT
    GCATGCATGCATGCATGCAT

Short runs stay uncoloured:

    AGGAGAGAGAA

Normal text stays uncoloured.


Runs of 12+ aa at >=90% letter purity and >=8 distinct letters:

    MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILS
    GSHMLEDPVGFAEAWKAQFPDSEPPRMELRSVGDIEQE


----------------------------------------------------------------
2.  Explicit color blocks
----------------------------------------------------------------

Force colouring on short or ambiguous fragments by wrapping them
in <color> ... </color> tags. 

<color>ACGTT</color>


----------------------------------------------------------------
3.  Conservation shading
----------------------------------------------------------------

Three or more rows of the same column / length / type get a
background highlight on conserved columns.

    seq1   MKTAYIAKQRQISFVKSHFSRQLEERLGL
    seq2   MKTAYEEKQRQISFVKSHFSRQLEERLGV
    seq3   MKTAYEKKQRQISFVKSHFSRQLEERLGI
    seq4   MKTAYIAKQRQISFV---FSRQLEKRLGL
    seq5   MRTAYIAKQKQISFVKSHFSRQLEERLGL


    hg38     ACGT--ACGTACG-ACGTACGT
    mm10     ACGT--ACGTACGTACGT-CGT
    rn6      ACGT--ACGTACGTACGTACGT
    canFam   ACGT--ACTTACGTACGTACGT
    panTro   ACGTAAACGTACG-ACGTACGT


----------------------------------------------------------------
4.  FASTQ data
----------------------------------------------------------------

FASTQ 4-line records are detected and colored. The quality line 
gets green intensity scaled to Phred score; hover over any quality
character to see Q value, error probability, and accuracy.

@read1 low->high quality ramp
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTA
+
!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
@read2 mostly high quality
GGGGCCCCAAAATTTTACGTACGTNNNNACGTACGTACGTA
+
IIIIIIIIIIIIIIHHHHHHHGGGGGF<<<EEEEDDDDCCC
