diff srf2fastq/io_lib-1.12.2/progs/append_sff.c @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/append_sff.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,124 @@
+/*
+ * Concatenates multiple SFF files together. It also strips out any indexing
+ * so this will need to be added again afterwards.
+ *
+ * The first argument is the archive to append to. All subsequent arguments
+ * are the archives to append to the first argument.
+ */
+
+#include <stdio.h>
+#include <string.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <io_lib/sff.h>
+#include <io_lib/os.h>
+
+#define BSIZE 1024*1024
+
+int main(int argc, char **argv) {
+    int i;
+    FILE *fpin, *fpout;
+    unsigned char *block;
+    unsigned char chdr[31];
+    sff_common_header *ch;
+
+    block = (unsigned char *)malloc(BSIZE);
+
+    if (argc < 3) {
+	fprintf(stderr, "Usage: append_sff sff_file add_me.sff ...\n");
+	return 1;
+    }
+
+    /* Open and decode the common header of the archive we'll append to */
+    if (NULL == (fpout = fopen(argv[1], "rb+"))) {
+	perror(argv[1]);
+	return 1;
+    }
+
+    if (31 != fread(chdr, 1, 31, fpout)) {
+	fprintf(stderr, "Couldn't read common header\n");
+	return 1;
+    }
+    ch = decode_sff_common_header(chdr);
+
+    /*
+     * Jump to the end of the archive or the start of the index.
+     * NB: If the index is not at the end we cannot use a simple append
+     * method.
+     */
+    fseek(fpout, 0, SEEK_END);
+    if (ch->index_len) {
+	if (ch->index_offset + ch->index_len != ftell(fpout)) {
+	    fprintf(stderr, "Index is not at the end of file => cannot append\n");
+	    return 1;
+	}
+	fseek(fpout, ch->index_offset, SEEK_SET);
+    }
+
+    /* Iterate around other archives, appending to the first one */
+    for (i = 2; i < argc; i++) {
+	sff_common_header *h;
+	uint64_t pos;
+	size_t len;
+	char *sff = argv[i];
+	int skipped;
+
+	printf("Copying %s\n", sff);
+
+	if (NULL == (fpin = fopen(sff, "rb"))) {
+	    perror(sff);
+	    return 1;
+	}
+
+	if (31 != fread(chdr, 1, 31, fpin)) {
+	    fprintf(stderr, "Couldn't read common header\n");
+	    return 1;
+	}
+
+	h = decode_sff_common_header(chdr);
+
+	/* Check if headers are compatible */
+	if (ch->flow_len        != h->flow_len ||
+	    ch->key_len         != h->key_len ||
+	    ch->flowgram_format != h->flowgram_format)
+	    fprintf(stderr, "*** Error: incompatible SFF headers ***\n");
+	fseek(fpin, h->header_len - 31, SEEK_CUR);
+	ch->nreads += h->nreads;
+
+	/* Copy all data from fpin to fpout, skipping index if present */
+	skipped = h->index_len ? 0 : 1;
+	for (pos = ftell(fpin); ; pos += len) {
+	    len = BSIZE;
+	    if (!skipped) {
+		if (pos == h->index_offset) {
+		    fseek(fpin, h->index_len, SEEK_CUR);
+		    pos += h->index_len;
+		    skipped = 1;
+		} else if (pos + BSIZE > h->index_offset) {
+		    len = h->index_offset - pos;
+		}
+	    }
+	    if (0 == (len = fread(block, 1, len, fpin)))
+		break;
+	    fwrite(block, 1, len, fpout);
+	}
+
+	free_sff_common_header(h);
+	fclose(fpin);
+    }
+
+    /* Seek back and update the header with the new nreads */
+    fseek(fpout, 0, SEEK_SET);
+    fread(chdr, 1, 31, fpout);
+    *(uint64_t *)(chdr+8)  = be_int8(0);
+    *(uint32_t *)(chdr+16) = be_int4(0);
+    *(uint32_t *)(chdr+20) = be_int4(ch->nreads);
+    fseek(fpout, 0, SEEK_SET);
+    fwrite(chdr, 1, 31, fpout);
+    fclose(fpout);
+
+    free_sff_common_header(ch);
+    free(block);
+
+    return 0;
+}