diff src/print_record.c @ 4:c70137414dcd draft

sickle v1.33

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/print_record.c	Wed Jul 23 18:35:10 2014 -0400
@@ -0,0 +1,42 @@
+#include <assert.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <zlib.h>
+#include <stdio.h>
+#include <unistd.h>
+#include "sickle.h"
+#include "kseq.h"
+
+
+void print_record (FILE *fp, kseq_t *fqr, cutsites *cs) {
+    fprintf(fp, "@%s", fqr->name.s);
+    if (fqr->comment.l) fprintf(fp, " %s\n", fqr->comment.s);
+    else fprintf(fp, "\n");
+    fprintf(fp, "%.*s\n", cs->three_prime_cut - cs->five_prime_cut, fqr->seq.s + cs->five_prime_cut);
+    fprintf(fp, "+\n");
+    fprintf(fp, "%.*s\n", cs->three_prime_cut - cs->five_prime_cut, fqr->qual.s + cs->five_prime_cut);
+}
+
+void print_record_gzip (gzFile fp, kseq_t *fqr, cutsites *cs) {
+    gzprintf(fp, "@%s", fqr->name.s);
+    if (fqr->comment.l) gzprintf(fp, " %s\n", fqr->comment.s);
+    else gzprintf(fp, "\n");
+    gzprintf(fp, "%.*s\n", cs->three_prime_cut - cs->five_prime_cut, fqr->seq.s + cs->five_prime_cut);
+    gzprintf(fp, "+\n");
+    gzprintf(fp, "%.*s\n", cs->three_prime_cut - cs->five_prime_cut, fqr->qual.s + cs->five_prime_cut);
+}
+
+void print_record_N (FILE *fp, kseq_t *fqr, int qualtype) {
+    fprintf(fp, "@%s", fqr->name.s);
+    if (fqr->comment.l) fprintf(fp, " %s\n", fqr->comment.s);
+    else fprintf(fp, "\n");
+    fprintf(fp, "N\n+\n%c\n", quality_constants[qualtype][Q_MIN]);
+}
+
+void print_record_N_gzip (gzFile fp, kseq_t *fqr, int qualtype) {
+    gzprintf(fp, "@%s", fqr->name.s);
+    if (fqr->comment.l) gzprintf(fp, " %s\n", fqr->comment.s);
+    else gzprintf(fp, "\n");
+    gzprintf(fp, "N\n+\n%c\n", quality_constants[qualtype][Q_MIN]);
+}
+