--- ./qual.c.orig 2008-11-12 17:45:48.000000000 +0100 +++ ./qual.c 2014-08-02 12:39:30.000000000 +0200 @@ -44,6 +44,12 @@ static int mismatch_LLR[256]; double *scaled_err_probs; /* used for finding high-quality segments */ +void read_qual(Database *); +void rescale_qual(Database *); +void incr_diff_hist(unsigned char *, unsigned char *, + int, int, int, int, + int, int, int, int ); + init_qual_arrays() { int i; @@ -580,6 +586,7 @@ } /* read in quality data */ +void read_qual(db) Database *db; { @@ -876,6 +883,7 @@ } /* NOT CORRECT WITH COMPRESSED QUAL */ +void rescale_qual(db) Database *db; { @@ -1153,6 +1161,10 @@ int conf_count[2], conf_max_score, conf_max_margin; /* # confirming reads */ } Diffsegnode; +void append_diffdata(Diffsegnode *); +void append_diffsegnode(Diffsegnode *, int, int, int, int, Diffsegnode *); +void write_diffsegnode(Diffsegnode *); + int data_type, data_length, data_qual, data_reverse, data_score, data_margin; unsigned char *data_seq; @@ -1400,6 +1412,7 @@ = n_align[i] = n_unalign[i] = n_p_unalign[i] = 0; } +void incr_diff_hist(seq, diff, length1, length2, start1, start2, end1, end2, reverse, ignore_ends) unsigned char *seq; unsigned char *diff; @@ -1543,6 +1556,7 @@ int node_index; extern unsigned char area_comp_mat[]; +void append_diffdata(diffsegnode) Diffsegnode *diffsegnode; { @@ -1607,6 +1621,7 @@ diffdata->count[!data_reverse] = 0; } +void append_diffsegnode(node, entry, seg_start, seg_end, conf_flag, data_node) Diffsegnode *node, *data_node; /* latter is 0 if reading from global vars */ int entry, seg_start, seg_end, conf_flag; @@ -1724,6 +1739,7 @@ strcpy(cdb, "CDSILRdi"); } +void write_diffsegnode(node) Diffsegnode *node; { @@ -1800,6 +1816,7 @@ write_diffsegnode(node->child[1]); } +void write_diffsegnodes() { int i;