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Author: Tim Booth <tbooth@ceh.ac.uk>
Last-Update: Thu, 19 Feb 2015 16:49:55 +0000
Description: Default Debian compiler options throw errors for
unused variables. This patch is removing those variables.
--- a/SeqPrep.c
+++ b/SeqPrep.c
@@ -69,7 +69,7 @@ void help ( char *prog_name ) {
fprintf(stderr, "\t-z <use mask; N will replace adapters>\n");
fprintf(stderr, "Optional Arguments for Merging:\n" );
fprintf(stderr, "\t-y <maximum quality score in output ((phred 33) default = '%c' )>\n", maximum_quality );
- fprintf(stderr, "\t-g <print overhang when adapters are present and stripped (use this if reads are different length)>\n");
+ fprintf(stderr, "\t-g <print overhang when adapters are present and stripped (use this if reads are different length)> - UNIMPLEMENTED\n");
fprintf(stderr, "\t-s <perform merging and output the merged reads to this file>\n" );
fprintf(stderr, "\t-E <write pretty alignments to this file for visual Examination>\n" );
fprintf(stderr, "\t-x <max number of pretty alignments to write (if -E provided); default = %d>\n", DEF_MAX_PRETTY_PRINT );
@@ -121,7 +121,7 @@ int main( int argc, char* argv[] ) {
char reverse_discard_fn[MAX_FN_LEN];
char merged_out_fn[MAX_FN_LEN];
bool do_read_merging = false;
- bool print_overhang = false;
+// bool print_overhang = false;
bool write_discard=false;
bool use_mask=false;
char forward_primer[MAX_SEQ_LEN+1];
@@ -266,7 +266,8 @@ int main( int argc, char* argv[] ) {
maximum_quality = optarg[0];
break;
case 'g' :
- print_overhang = true;
+ //print_overhang is never used!
+ //print_overhang = true;
break;
case 's' :
do_read_merging = true;
--- a/stdaln.c
+++ b/stdaln.c
@@ -545,13 +545,12 @@ int aln_local_core(unsigned char *seq1,
int start, end, max_score;
int thres, *suba, *ss;
- int gap_open, gap_ext, b;
+ int gap_open, gap_ext;
int *score_matrix, N_MATRIX_ROW;
/* initialize some align-related parameters. just for compatibility */
gap_open = ap->gap_open;
gap_ext = ap->gap_ext;
- b = ap->band_width;
score_matrix = ap->matrix;
N_MATRIX_ROW = ap->row;
thres = _thres > 0? _thres : -_thres;
@@ -865,7 +864,7 @@ uint16_t *aln_path2cigar(const path_t *p
int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
path_t *path, int *path_len, int G0, uint8_t *_mem)
{
- int q, r, qr, tmp_len;
+ int q, r, qr;
int32_t **s_array, *score_array;
int is_overflow, of_base;
uint32_t *eh;
@@ -892,7 +891,6 @@ int aln_extend_core(unsigned char *seq1,
s_array[i] = (int32_t*)_p, _p += 4 * len1;
/* initialization */
aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array);
- tmp_len = len1 + 1;
start = 1; end = 2;
end_i = end_j = 0;
score = 0;
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