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embed samtools sources directly, since Rsamtools has moved to htslib

Michael Lawrence authored on 11/02/2019 20:33:07
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new file mode 100644
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+#include <stdio.h>
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+#include <stdlib.h>
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+#include "knetfile.h"
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+#include "bgzf.h"
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+#include "bam.h"
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+
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+#define BUF_SIZE 0x10000
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+
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+int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
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+{
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+	BGZF *fp;
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+	bam_header_t *old;
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+	int len;
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+	uint8_t *buf;
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+	if (in->is_write) return -1;
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+	buf = malloc(BUF_SIZE);
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+	old = bam_header_read(in);
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+	fp = bgzf_fdopen(fd, "w");
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+	bam_header_write(fp, h);
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+	if (in->block_offset < in->block_length) {
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+		bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
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+		bgzf_flush(fp);
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+	}
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+#ifdef _USE_KNETFILE
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+	while ((len = knet_read(in->fp, buf, BUF_SIZE)) > 0)
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+		fwrite(buf, 1, len, fp->fp);
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+#else
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+	while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
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+		fwrite(buf, 1, len, fp->file);
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+#endif
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+	free(buf);
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+	fp->block_offset = in->block_offset = 0;
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+	bgzf_close(fp);
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+	return 0;
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+}
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+
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+#ifdef _MAIN                    /* Rsamtools */
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+int main_reheader(int argc, char *argv[])
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+{
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+	bam_header_t *h;
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+	BGZF *in;
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+	if (argc != 3) {
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+		fprintf(stderr, "Usage: samtools reheader <in.header.sam> <in.bam>\n");
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+		return 1;
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+	}
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+	{ // read the header
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+		tamFile fph = sam_open(argv[1]);
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+		if (fph == 0) {
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+			fprintf(stderr, "[%s] fail to read the header from %s.\n", __func__, argv[1]);
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+			return 1;
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+		}
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+		h = sam_header_read(fph);
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+		sam_close(fph);
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+	}
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+	in = strcmp(argv[2], "-")? bam_open(argv[2], "r") : bam_dopen(fileno(stdin), "r");
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+	if (in == 0) {
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+		fprintf(stderr, "[%s] fail to open file %s.\n", __func__, argv[2]);
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+		return 1;
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+	}
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+	bam_reheader(in, h, fileno(stdout));
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+	bgzf_close(in);
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+	return 0;
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+}
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+#endif  /* Rsamtools */