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Prophex filter #22

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Prophex filter #22

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60a1b96
Fix bugs and style
salikhov-kamil Aug 2, 2018
4017cd9
Add tests/A14_filter
salikhov-kamil Aug 2, 2018
aaf1edb
Rename parameters
karel-brinda Oct 25, 2018
e2cae8d
Fix formatting fastq output
karel-brinda Oct 25, 2018
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Fix bugs and style
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@salikhov-kamil
salikhov-kamil committed Aug 2, 2018
commit 60a1b96ad5d56e8caff48b46bbbbe0cd1c8cb099
107 changes: 99 additions & 8 deletions src/main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@ static int usage() {
fprintf(stderr, "\n");
fprintf(stderr, "Command: index construct a BWA index and k-LCP\n");
fprintf(stderr, " query query reads against index\n");
fprintf(stderr, " filter filter reads\n");
fprintf(stderr, "\n");
fprintf(stderr, " klcp construct an additional k-LCP\n");
fprintf(stderr, " bwtdowngrade downgrade .bwt to the old, more compact format without Occ\n");
Expand All @@ -45,10 +46,10 @@ static int usage_klcp() {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: prophex klcp [options] <idxbase>\n");
fprintf(stderr, "\n");
fprintf(stderr, "Options: -k INT length of k-mer\n");
fprintf(stderr, "Options: -k INT length of k-mer\n");
fprintf(stderr, " -s construct k-LCP and SA in parallel\n");
fprintf(stderr, " -i sampling distance for SA\n");
fprintf(stderr, " -h print help message\n");
fprintf(stderr, " -i sampling distance for SA\n");
fprintf(stderr, " -h print help message\n");
fprintf(stderr, "\n");
return 1;
}
Expand All @@ -67,14 +68,32 @@ static int usage_index() {
static int usage_bwtdowngrade() {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: prophex bwtdowngrade <input.bwt> <output.bwt>\n");
fprintf(stderr, " -h print help message\n");
fprintf(stderr, "Options: -h print help message\n");
fprintf(stderr, "\n");
return 1;
}

static int usage_bwt2fa() {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: prophex bwt2fa <idxbase> <output.fa>\n");
fprintf(stderr, "Options: -h print help message\n");
fprintf(stderr, "\n");
return 1;
}

static int usage_filter(int threads) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: prophex filter [options] <idxbase> <in.fq>\n");
fprintf(stderr, "\n");
fprintf(stderr, "Options: -k INT length of k-mer\n");
fprintf(stderr, " -u use k-LCP for querying\n");
fprintf(stderr, " -b print sequences and base qualities\n");
fprintf(stderr, " -l STR log file name to output statistics\n");
fprintf(stderr, " -t INT number of threads [%d]\n", threads);
fprintf(stderr, " -m FLOAT keep only reads with proportion of matches >= FLOAT [0.3]\n");
fprintf(stderr, " -n INT keep only reads with number of matches >= INT (ignored if -m is set)\n");
fprintf(stderr, " -o prefix for fastq for passing reads\n");
fprintf(stderr, " -f prefix for fastq for filtered reads\n");
fprintf(stderr, " -h print help message\n");
fprintf(stderr, "\n");
return 1;
Expand All @@ -96,13 +115,86 @@ static int usage_query(int threads) {
return 1;
}

int prophex_filter(int argc, char *argv[]) {
int c;
prophex_opt_t *opt;
char *prefix;
int usage = 0;
opt = prophex_init_opt();
opt->is_query = 0;
int m_set = 0;
int n_set = 0;
while ((c = getopt(argc, argv, "l:puvk:bt:hm:n:o:f:")) >= 0) {
switch (c) {
case 'u':
opt->use_klcp = 1;
break;
case 'k':
opt->kmer_length = atoi(optarg);
break;
case 'l': {
opt->need_log = 1;
opt->log_file_name = optarg;
break;
}
case 'b':
opt->output_read_qual = 1;
break;
case 't':
opt->n_threads = atoi(optarg);
break;
case 'h':
usage = 1;
break;
case 'm':
opt->match_proportion = atof(optarg);
m_set = 1;
break;
case 'n':
opt->match_number = atoi(optarg);
n_set = 1;
break;
case 'o':
opt->passed_reads_file_name = optarg;
break;
case 'f':
opt->filtered_reads_file_name = optarg;
break;
default:
return 1;
}
}
if (n_set && !m_set) {
opt->match_proportion = -1;
}
if (usage) {
usage_filter(opt->n_threads);
return 0;
}

if (optind + 2 > argc) {
usage_filter(opt->n_threads);
return 1;
}
if ((prefix = bwa_idx_infer_prefix(argv[optind])) == 0) {
fprintf(stderr, "[prophex:%s] fail to locate the index %s\n", __func__, argv[optind]);
free(opt);
return 1;
}
query(prefix, argv[optind + 1], opt);
free(opt);
free(prefix);
return 0;
}

int prophex_query(int argc, char *argv[]) {
int c;
prophex_opt_t *opt;
char *prefix;
int usage = 0;
opt = prophex_init_opt();
while ((c = getopt(argc, argv, "l:psuvk:bt:h")) >= 0) {
opt->is_query = 1;
while ((c = getopt(argc, argv, "l:puvk:bt:h")) >= 0) {
switch (c) {
case 'v': {
opt->output_old = 1;
Expand All @@ -114,9 +206,6 @@ int prophex_query(int argc, char *argv[]) {
case 'k':
opt->kmer_length = atoi(optarg);
break;
case 's':
opt->skip_after_fail = 1;
break;
case 'p':
opt->skip_positions_on_border = 0;
break;
Expand Down Expand Up @@ -333,6 +422,8 @@ int main(int argc, char *argv[]) {
ret = prophex_klcp(argc - 1, argv + 1);
else if (strcmp(argv[1], "query") == 0)
ret = prophex_query(argc - 1, argv + 1);
else if (strcmp(argv[1], "filter") == 0)
ret = prophex_filter(argc - 1, argv + 1);
else if (strcmp(argv[1], "index") == 0)
ret = prophex_index(argc - 1, argv + 1);
else if (strcmp(argv[1], "bwtdowngrade") == 0)
Expand Down
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