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.
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
COLORdictionary 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.