4 * Created on: Oct 14, 2009
17 const char *read, // ASCII colors, '0', '1', '2', '3', '.'
18 const char *qual, // ASCII quals, Phred+33 encoded
19 size_t readi, // offset of first character within 'read' to consider
20 size_t readf, // offset of last char (exclusive) in 'read' to consider
21 const char *ref, // reference sequence, as masks
22 size_t refi, // offset of first character within 'ref' to consider
23 size_t reff, // offset of last char (exclusive) in 'ref' to consider
24 int snpPhred, // penalty incurred by a SNP
25 char *ns, // decoded nucleotides are appended here
26 char *cmm, // where the color mismatches are in the string
27 char *nmm, // where nucleotide mismatches are in the string
28 int& cmms, // number of color mismatches
29 int& nmms);// number of nucleotide mismatches
31 #endif /* COLOR_DEC_H_ */