internalising dependencies

bin/Makefile

@@ -0,0 +1,12 @@
+# A simple Makefile to compile the C code here
+#
+
+FLAGS := $(FLAGS) -Wall -O3
+override CFLAGS += $(shell pkg-config --cflags --libs python3-embed)
+
+all:
+	gcc $(FLAGS) -o fastq2fasta fastq2fasta.c -lz
+
+clean:
+	rm -f fastq2fasta 
+

bin/fastq2fasta.c

@@ -0,0 +1,119 @@
+/* Average the quality scores in a fastq file 
+ *
+ * Rob Edwards, 10/12/21
+ *
+ */
+
+
+#include <zlib.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <string.h>
+#include "kseq.h"
+
+KSEQ_INIT(gzFile, gzread)
+
+#define table_size 10000
+
+void helpme() {
+  fprintf(stderr,
+      "fastq2fasta [options] <fastq file> <fasta file>\n"
+      "Use  - for either input or output to use STDIN/STDOUT\n"
+      "Options:\n"
+      "\t-r replace spaces in the fasta header line with '_'\n"
+      "\t-n <1/2> add the read number to the header line at the first space\n"
+   );
+}
+
+int main(int argc, char *argv[]) {
+
+	if ( argc < 2) {
+		helpme();
+		return 1;
+	}
+
+
+	int replace = 0;
+	char *n = NULL;
+
+	for (;;) {
+		switch(getopt(argc, argv, "rn:")) {
+			default:
+				helpme();
+				return 1;
+			case -1:
+				break;
+			case 'r':
+				replace = 1;
+				continue;
+			case 'n':
+				n = optarg;
+				continue;
+		}
+		break;
+	}
+
+	if (optind +2 != argc) {
+		helpme();
+		return 1;
+	}
+
+	char* fqf = argv[optind];
+	char* faf = argv[optind+1]; 
+
+	FILE *fw;
+	kseq_t *seq;
+
+
+	FILE *instream = NULL;
+
+	if (strcmp(fqf, "-") !=0) {
+		instream = fopen(fqf, "r");
+		if (instream == NULL) {
+			fprintf(stderr, "ERROR: Can't open %s\n", fqf);
+			return 1;
+		}
+	}
+	else
+		instream = stdin;
+	gzFile fp = gzdopen(fileno(instream), "r");
+	if (fp == NULL) {
+		fprintf(stderr, "ERROR: There was a problem opening the stream to %s\n", fqf);
+		return 1;
+	}
+
+
+	if (strcmp(faf, "-") != 0)
+		fw = fopen(faf, "w");
+	else
+		fw = stdout;
+
+	seq = kseq_init(fp);
+	int l;
+	while ((l = kseq_read(seq)) >= 0) {
+		if (seq->comment.l == 0) {
+			seq->comment.s = malloc(1);
+			seq->comment.s = '\0';
+		}
+		if (replace) {
+			for (long unsigned int i = 0; i <= strlen(seq->comment.s); i++) {
+				if (seq->comment.s[i] == ' ') {
+					seq->comment.s[i] = '_';
+				}
+			}
+			fprintf(fw, ">%s_%s\n%s\n", seq->name.s, seq->comment.s, seq->seq.s);
+		}
+		else if (n) {
+			fprintf(fw, ">%s/%s %s\n%s\n", seq->name.s, n, seq->comment.s, seq->seq.s);
+		}
+		else {
+			fprintf(fw, ">%s %s\n%s\n", seq->name.s, seq->comment.s, seq->seq.s);
+		}
+	}
+	kseq_destroy(seq);
+	gzclose(fp);
+	fclose(fw);
+}
+
+