print_bed is back

dputhier · Jan 16, 2019 · 9ffb3c9 · 9ffb3c9
1 parent 4193cf4
commit 9ffb3c9
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Showing 2 changed files with 30 additions and 3 deletions.
diff --git a/command/free_gtf_data.c b/command/free_gtf_data.c
@@ -65,9 +65,6 @@ int free_gtf_data(GTF_DATA *gtf_data) {
 			free(row->field);
 
 			for (j = 0; j < row->attributes.nb; j++) {
-				//if (row->attributes.attr[j]->key != NULL) free(row->attributes.attr[j]->key);
-				//if (row->attributes.attr[j]->value != NULL) free(row->attributes.attr[j]->value);
-				//free(row->attributes.attr[j]);
 				if ((row->attributes.attr + j)->key != NULL) free((row->attributes.attr + j)->key);
 				if ((row->attributes.attr + j)->value != NULL) free((row->attributes.attr + j)->value);
 			}

diff --git a/command/print_bed.c b/command/print_bed.c
@@ -0,0 +1,30 @@
+/*
+ * write_bed.c
+ *
+ *  Created on: December 7, 2018
+ *      Author: puthier (based on Fafa code...)
+ *  Objective: print a gtf obj in bed format
+ */
+
+#include "libgtftk.h"
+
+extern void print_row_bed(FILE *output, GTF_ROW *r, char delim, int add_chr, char *keys, char *sep, char *more_info);
+
+__attribute__ ((visibility ("default")))
+void *print_bed(GTF_DATA *gtf_data, char *output, int add_chr, char *keys, char *sep, char *more_info) {
+	int i;
+	FILE *out = stdout;
+
+	if (gtf_data != NULL) {
+		if (*output != '-') out = fopen(output, "w");
+		if (out == NULL) out = stdout;
+		for (i = 0; i < gtf_data->size; i++){
+		    print_row_bed(out, gtf_data->data[i], '\t', add_chr, keys, sep, more_info);
+		}
+		if (out != stdout) {
+			fflush(out);
+			fclose(out);
+		}
+	}
+	return 0;
+}