support for reference sequences with lowercase characters (a, c, g, t)

[tkonopka]

This addresses issue #18. It fixes problems rendering reference sequences with lowercase characters.

The fix comes in two parts. First is an expansion of the COLOR dictionary to associate hex codes to each of the lowercase bases. All the colors are defined separately. This is makes the code long, but leaves the option to tune the colors later.

The second part is an adjustment in the drawing of the coverage track. Without this edit, the coverage track signals discrepancies between bases in reads (uppercase) and the reference. The images below show a random sequence with made-up reads, before and after implementing the edit.

To reproduce, here is a random reference sequence and two reads in sam format.

>random_with_lowercase
caAagTGtgCACCAtTTCtCactaacaGGCGgtaTaAAgtgatAGTtagaaTTTgaagaT
gATTAAggcTgctGGtGtGTGaTAtcGgtcaGaTatgaTAaCagagAaCCcCTcgatgtt
aAgAGgTTtCaaCatGGgTtgaaAcTaccgtgCTtTgTtTGgtGaTTTcatttctcaGAC
aTTaCAgTcGGggtGtGaTCGgtGgtGCcgGTcATAgATAACGCtaAgTgGcGacGGtGa
gAaAAcGCtgCAattgaaaGtgGcacgacGACgCTGacCtccCaGtGTGgACgGgTaCtg
ttgcaaacGCagtTtACcgGGATaTAAaTTgGGGCcccaGAggAaAGaTgcTCCagATCg
aGTGcgGAGCtTGCGttaaGCcATTgCcaTaGGTAggcttcGAGTcaCTTCcAAcCGATT
taAcGgGtaTAGAtGtTgcTGAGgGaCaTtTCATtcCAcACTCatGcttTAGtaacCcTt
cGGCaacatCcagtAtagtTtcTgAgcTgctaCttCatAgaTTgAAcTGACCGgACaAcA
ctACTGCGTattCatgcCGCctCCCcccCaAGtCCTGacAccgggtaggtataTGTacGA
aagGgTcAcaTTtTcCgcAtcaggcgCCGCgTTATGaCGtCTTcGGAcaTCTtGcGTAgG
agtcCacaaTAagccCCtaAgCTttAcTtAGccGgagtTcAaAGAGaATGCcGCGGcGCA
AgCTgggtccTTgtttAGAaATgTGCAAATtGGAGGtTtAtCACTTTGgTtaGTcGaTaT
gTTcgGgAtTAccttTaCGctgataGGaGcaTcccgAcTccAtAtctaGGgGCcCtGgcA
CTATGaAGTCTAatAgTaGTggTTCtCaaaCGCTccgtGTccagTTGCacATCcTACTCT
CTGAcTGctGagcCcgaTGCcctGtCgtAAatGACgcaGCcAgGGGTGtcTActggGCtg
CcgaCCgacccttAcGTTtacgaacggGATctacGtTTgAcGCATcAgCAGCAAaGaTAA
CTGaATGacgCtgTCAgtcTaGTActCcAACAaAAGTtcGtGCTTtGGCCGAGAggGgcC
tAcgtgGcGAcAaCaAaCtaGAATAacATAaaaAtCaagGtCgGcgtgggtgcAtCcgtT
gTtGCGAtCttttTttAAgtGGActaCgTtgcTttCgAcaATccCGtccgAgTCCActgC
aCaTgGGAGtTgTtaGTCTtccacAagTcCaCtgctGtcTAaAcTacTAGatgAaAGTCC
ACaggacTaaatctcaAAcAAGcTACtGCCAaaCAtTggTtATGTtAgaAGttGtGGATC
CCACtGCggtaTaataggCgccCgtAGGGGCggAAcctGCtcgCtgtgGGTcTTgtaGGa
GcAcgGAcACCgaGcGAcGGcgGttTctGtgccAgCACaCgttCTtTgcgaGaTagGttC

@SQ	SN:random_with_lowercase	LN:1440
@PG	ID:bwa	PN:bwa	VN:0.7.17-r1188	CL:bwa mem -o example.sam large.fa example.fastq
random_with_lowercase:600-630	0	random_with_lowercase	600	60	31M	*	0	0	AAAGGGTCACATTTTCCGCATCAGGCGCCGC	sssssssssssssssssssssssssssssss	NM:i:0	MD:Z:31	AS:i:31	XS:i:0
random_with_lowercase:620-650	0	random_with_lowercase	620	60	31M	*	0	0	TCAGGCGCCGCGTTATGACGTCTTCGGACAT	sssssssssssssssssssssssssssssss	NM:i:0	MD:Z:31	AS:i:31	XS:i:0

[nr23730]

This is very helpful! I would like to see this merged.
By the way: This fixes #22 and #18.

[blaiseli]

@danielmsk Could you accept this pull request ? This might make your software much easier to use for some people.

Thanks in advance.

[danielmsk]

Thanks for the fix! @tkonopka