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ignore stripping of primer(barcode) sequences #8

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ignore stripping of primer(barcode) sequences #8

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28 changes: 20 additions & 8 deletions src/demulti_paired.c
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ static struct option paired_long_options[] = {
{"unknown-output1", required_argument, 0, 'u'},
{"unknown-output2", required_argument, 0, 'w'},
{"both-barcodes", optional_argument, 0, 'c'},
{"strip-primers", optional_argument, 0, 's'},
{"max-mismatch", optional_argument, 0, 'm'},
{"quiet", optional_argument, 0, 'z'},
{GETOPT_HELP_OPTION_DECL},
Expand All @@ -37,6 +38,7 @@ Options:\n\
fprintf (stderr, "-u, --unknown-output1, Output paired-end file 1 that contains records with no barcodes found. (required)\n\
-w, --unknown-output2, Output paired-end file 2 that contains records with no barcodes found. (required)\n\
-c, --both-barcodes, Optional flag that indicates that both fastq files have barcodes.\n\
-s, --strip-primers, Optional flag that indicates if primers should be stripped off sequences.\n\
-m <n>, --max-mismatch <n>, Optional argument that is the maximum number of mismatches allowed in a barcode. Default 0.\n");

fprintf (stderr, "--quiet, don't print barcode matching info\n\
Expand Down Expand Up @@ -65,6 +67,7 @@ int paired_main (int argc, char *argv[]) {
char *unknownfn1=NULL;
char *unknownfn2=NULL;
int both_have_barcodes=0;
int strip_primers=0;
barcode_data_paired *curr, *head, *temp;
char barcode [MAX_BARCODE_LENGTH];
char baroutfn1 [MAX_FILENAME_LENGTH];
Expand All @@ -77,7 +80,7 @@ int paired_main (int argc, char *argv[]) {

while (1) {
int option_index = 0;
optc = getopt_long (argc, argv, "dcf:r:b:u:w:m:z", paired_long_options, &option_index);
optc = getopt_long (argc, argv, "dcf:r:b:u:w:m:z:s", paired_long_options, &option_index);

if (optc == -1) break;

Expand Down Expand Up @@ -112,6 +115,10 @@ int paired_main (int argc, char *argv[]) {
case 'c':
both_have_barcodes=1;
break;

case 's':
strip_primers=1;
break;

case 'm':
mismatch = atoi (optarg);
Expand Down Expand Up @@ -227,30 +234,35 @@ int paired_main (int argc, char *argv[]) {
fprintf (curr->bcfile1, "@%s", fqrec1->name.s);
if (fqrec1->comment.l) fprintf (curr->bcfile1, " %s\n", fqrec1->comment.s);
else fprintf (curr->bcfile1, "\n");

fprintf (curr->bcfile1, "%s\n", (fqrec1->seq.s)+strlen(curr->bc));
if(!strip_primers) fprintf (curr->bcfile1, "%s\n", fqrec1->seq.s);
else fprintf (curr->bcfile1, "%s\n", (fqrec1->seq.s)+strlen(curr->bc));

fprintf (curr->bcfile1, "+%s", fqrec1->name.s);
if (fqrec1->comment.l) fprintf (curr->bcfile1, " %s\n", fqrec1->comment.s);
else fprintf (curr->bcfile1, "\n");

fprintf (curr->bcfile1, "%s\n", (fqrec1->qual.s)+strlen(curr->bc));

if(!strip_primers) fprintf (curr->bcfile1, "%s\n", fqrec1->qual.s);
else fprintf (curr->bcfile1, "%s\n", (fqrec1->qual.s)+strlen(curr->bc));

fprintf (curr->bcfile2, "@%s", fqrec2->name.s);
if (fqrec2->comment.l) fprintf (curr->bcfile2, " %s\n", fqrec2->comment.s);
else fprintf (curr->bcfile2, "\n");

if (!both_have_barcodes) fprintf (curr->bcfile2, "%s\n", fqrec2->seq.s);
else fprintf (curr->bcfile2, "%s\n", (fqrec2->seq.s)+strlen(curr->bc));
else {
if(!strip_primers) fprintf (curr->bcfile2, "%s\n", fqrec2->seq.s);
else fprintf (curr->bcfile2, "%s\n", (fqrec2->seq.s)+strlen(curr->bc));
}

fprintf (curr->bcfile2, "+%s", fqrec2->name.s);
if (fqrec2->comment.l) fprintf (curr->bcfile2, " %s\n", fqrec2->comment.s);
else fprintf (curr->bcfile2, "\n");

if (!both_have_barcodes) fprintf (curr->bcfile2, "%s\n", fqrec2->qual.s);
else fprintf (curr->bcfile2, "%s\n", (fqrec2->qual.s)+strlen(curr->bc));

else {
if(!strip_primers) fprintf (curr->bcfile2, "%s\n", fqrec2->qual.s);
else fprintf (curr->bcfile2, "%s\n", (fqrec2->qual.s)+strlen(curr->bc));
}
curr->num_records += 2;
}

Expand Down