/*
* Reads a file and outputs a new CRAM file to stdout with 'h'
* replaced as the header. No checks are made to the validity.
*
* FIXME: error checking
*/
int cram_reheader(cram_fd *in, bam_hdr_t *h, const char *arg_list, int add_PG)
{
htsFile *h_out = hts_open("-", "wc");
cram_fd *out = h_out->fp.cram;
cram_container *c = NULL;
int ret = -1;
// Attempt to fill out a cram->refs[] array from @SQ headers
cram_fd_set_header(out, sam_hdr_parse_(h->text, h->l_text));
if (add_PG) {
if (sam_hdr_add_PG(cram_fd_get_header(out), "samtools",
"VN", samtools_version(),
arg_list ? "CL": NULL,
arg_list ? arg_list : NULL,
NULL) != 0)
goto err;
// Covert back to bam_hdr_t struct
free(h->text);
h->text = strdup(sam_hdr_str(cram_fd_get_header(out)));
h->l_text = sam_hdr_length(cram_fd_get_header(out));
if (!h->text)
goto err;
}
if (sam_hdr_write(h_out, h) != 0)
goto err;
cram_set_option(out, CRAM_OPT_REFERENCE, NULL);
while ((c = cram_read_container(in))) {
int32_t i, num_blocks = cram_container_get_num_blocks(c);
if (cram_write_container(out, c) != 0)
goto err;
for (i = 0; i < num_blocks; i++) {
cram_block *blk = cram_read_block(in);
if (!blk || cram_write_block(out, blk) != 0) {
if (blk) cram_free_block(blk);
goto err;
}
cram_free_block(blk);
}
cram_free_container(c);
}
ret = 0;
err:
if (hts_close(h_out) != 0)
ret = -1;
return ret;
}
/*
* Reads a file and outputs a new BAM file to fd with 'h' replaced as
* the header. No checks are made to the validity.
*/
int bam_reheader(BGZF *in, bam_hdr_t *h, int fd,
const char *arg_list, int add_PG)
{
BGZF *fp;
ssize_t len;
uint8_t *buf;
if (in->is_write) return -1;
buf = malloc(BUF_SIZE);
if (bam_hdr_read(in) == NULL) {
fprintf(stderr, "Couldn't read header\n");
free(buf);
return -1;
}
fp = bgzf_fdopen(fd, "w");
if (add_PG) {
// Around the houses, but it'll do until we can manipulate bam_hdr_t natively.
SAM_hdr *sh = sam_hdr_parse_(h->text, h->l_text);
if (sam_hdr_add_PG(sh, "samtools",
"VN", samtools_version(),
arg_list ? "CL": NULL,
arg_list ? arg_list : NULL,
NULL) != 0)
return -1;
free(h->text);
h->text = strdup(sam_hdr_str(sh));
h->l_text = sam_hdr_length(sh);
if (!h->text)
return -1;
sam_hdr_free(sh);
}
bam_hdr_write(fp, h);
if (in->block_offset < in->block_length) {
bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
bgzf_flush(fp);
}
while ((len = bgzf_raw_read(in, buf, BUF_SIZE)) > 0)
bgzf_raw_write(fp, buf, len);
free(buf);
fp->block_offset = in->block_offset = 0;
bgzf_close(fp);
return 0;
}
int main(int argc, char **argv) {
cram_fd *fd;
bam_file_t *bfd;
bam_seq_t *bam = NULL;
char mode[4] = {'w', '\0', '\0', '\0'};
char *prefix = NULL;
int decode_md = 0;
int C;
int start, end;
char ref_name[1024] = {0}, *arg_list, *ref_fn = NULL;
int embed_ref = 0;
while ((C = getopt(argc, argv, "bu0123456789mp:hr:R:X")) != -1) {
switch (C) {
case 'b':
mode[1] = 'b';
break;
case 'u':
mode[2] = '0';
break;
case '0': case '1': case '2': case '3': case '4':
case '5': case '6': case '7': case '8': case '9':
mode[2] = C;
break;
case 'm':
decode_md = 1;
break;
case 'p':
prefix = optarg;
break;
case 'h':
usage(stdout);
return 0;
case 'r':
ref_fn = optarg;
break;
case 'X':
embed_ref = 1;
break;
case 'R': {
char *cp = strchr(optarg, ':');
if (cp) {
*cp = 0;
switch (sscanf(cp+1, "%d-%d", &start, &end)) {
case 1:
end = start;
break;
case 2:
break;
default:
fprintf(stderr, "Malformed range format\n");
return 1;
}
} else {
start = INT_MIN;
end = INT_MAX;
}
strncpy(ref_name, optarg, 1023);
break;
}
case '?':
fprintf(stderr, "Unrecognised option: -%c\n", optopt);
usage(stderr);
return 1;
}
}
if (argc - optind != 1 && argc - optind != 2) {
usage(stderr);
return 1;
}
if (argc - optind == 1) {
if (NULL == (bfd = bam_open("-", mode))) {
fprintf(stderr, "Failed to open SAM/BAM output\n.");
return 1;
}
} else {
if (NULL == (bfd = bam_open(argv[optind+1], mode))) {
fprintf(stderr, "Failed to open SAM/BAM output\n.");
perror(argv[optind+1]);
return 1;
}
}
if (NULL == (fd = cram_open(argv[optind], "rb"))) {
fprintf(stderr, "Error opening CRAM file '%s'.\n", argv[optind]);
return 1;
}
if (*ref_name != 0)
cram_index_load(fd, argv[optind]);
if (prefix)
cram_set_option(fd, CRAM_OPT_PREFIX, prefix);
if (decode_md)
cram_set_option(fd, CRAM_OPT_DECODE_MD, decode_md);
if (embed_ref)
cram_set_option(fd, CRAM_OPT_EMBED_REF, embed_ref);
/* Find and load reference */
cram_load_reference(fd, ref_fn);
if (!fd->refs && !embed_ref) {
fprintf(stderr, "Unable to find an appropriate reference.\n"
"Please specify a valid reference with -r ref.fa option.\n");
return 1;
}
bfd->header = fd->header;
if (*ref_name != 0) {
cram_range r;
int refid = sam_hdr_name2ref(fd->header, ref_name);
if (refid == -1 && *ref_name != '*') {
fprintf(stderr, "Unknown reference name '%s'\n", ref_name);
return 1;
}
r.refid = refid;
r.start = start;
r.end = end;
cram_set_option(fd, CRAM_OPT_RANGE, &r);
}
/* SAM Header */
if (!(arg_list = stringify_argv(argc, argv)))
return 1;
sam_hdr_add_PG(bfd->header, "cram_to_sam",
"VN", PACKAGE_VERSION,
"CL", arg_list, NULL);
free(arg_list);
bam_write_header(bfd);
while (cram_get_bam_seq(fd, &bam) == 0) {
bam_put_seq(bfd, bam);
}
if (!cram_eof(fd)) {
fprintf(stderr, "Error while reading file\n");
return 1;
}
cram_close(fd);
bfd->header = NULL;
bam_close(bfd);
free(bam);
return 0;
}
int main(int argc, char **argv) {
scram_fd *in, *out;
bam_seq_t *s;
char imode[10], *in_f = "", omode[10], *out_f = "";
int level = '\0'; // nul terminate string => auto level
int c, verbose = 0;
int s_opt = 0, S_opt = 0, embed_ref = 0, ignore_md5 = 0, decode_md = 0;
char *ref_fn = NULL;
int start, end, multi_seq = -1, no_ref = 0;
int use_bz2 = 0, use_arith = 0, use_lzma = 0;
char ref_name[1024] = {0};
refs_t *refs;
int nthreads = 1;
t_pool *p = NULL;
int max_reads = -1;
enum quality_binning binning = BINNING_NONE;
/* Parse command line arguments */
while ((c = getopt(argc, argv, "u0123456789hvs:S:V:r:xXeI:O:R:!MmjJZt:BN:")) != -1) {
switch (c) {
case '0': case '1': case '2': case '3': case '4':
case '5': case '6': case '7': case '8': case '9':
level = c;
break;
case 'u':
level = '0';
break;
case 'h':
usage(stdout);
return 0;
case 'v':
verbose++;
break;
case 's':
s_opt = atoi(optarg);
break;
case 'S':
S_opt = atoi(optarg);
break;
case 'm':
decode_md = 1;
break;
case 'V':
if (cram_set_option(NULL, CRAM_OPT_VERSION, optarg))
return 1;
break;
case 'r':
ref_fn = optarg;
break;
case 'X':
fprintf(stderr, "-X is deprecated in favour of -e.\n");
case 'e':
embed_ref = 1;
break;
case 'x':
no_ref = 1;
break;
case 'I':
in_f = parse_format(optarg);
break;
case 'O':
out_f = parse_format(optarg);
break;
case 'R': {
char *cp = strchr(optarg, ':');
if (cp) {
*cp = 0;
switch (sscanf(cp+1, "%d-%d", &start, &end)) {
case 1:
end = start;
break;
case 2:
break;
default:
fprintf(stderr, "Malformed range format\n");
return 1;
}
} else {
start = INT_MIN;
end = INT_MAX;
}
strncpy(ref_name, optarg, 1023);
break;
}
case '!':
ignore_md5 = 1;
break;
case 'M':
multi_seq = 1;
break;
case 'j':
#ifdef HAVE_LIBBZ2
use_bz2 = 1;
#else
fprintf(stderr, "Warning: bzip2 support is not compiled into this"
" version.\nPlease recompile.\n");
#endif
break;
case 'J':
use_arith = 1;
break;
case 'Z':
#ifdef HAVE_LIBLZMA
use_lzma = 1;
#else
fprintf(stderr, "Warning: lzma support is not compiled into this"
" version.\nPlease recompile.\n");
#endif
break;
case 't':
nthreads = atoi(optarg);
if (nthreads < 1) {
fprintf(stderr, "Number of threads needs to be >= 1\n");
return 1;
}
break;
case 'B':
binning = BINNING_ILLUMINA;
break;
case 'N': // For debugging
max_reads = atoi(optarg);
break;
case '?':
fprintf(stderr, "Unrecognised option: -%c\n", optopt);
usage(stderr);
return 1;
}
}
if (argc - optind > 2) {
fprintf(stderr, "Usage: scramble [input_file [output_file]]\n");
return 1;
}
/* Open up input and output files */
sprintf(imode, "r%s%c", in_f, level);
if (argc - optind > 0) {
if (*in_f == 0)
sprintf(imode, "r%s%c", detect_format(argv[optind]), level);
if (!(in = scram_open(argv[optind], imode))) {
fprintf(stderr, "Failed to open file %s\n", argv[optind]);
return 1;
}
} else {
if (!(in = scram_open("-", imode))) {
fprintf(stderr, "Failed to open file %s\n", argv[optind]);
return 1;
}
}
if (!in->is_bam && ref_fn) {
cram_load_reference(in->c, ref_fn);
if (!in->c->refs && !embed_ref) {
fprintf(stderr, "Unable to find an appropriate reference.\n"
"Please specify a valid reference with "
"-r ref.fa option.\n");
return 1;
}
}
sprintf(omode, "w%s%c", out_f, level);
if (argc - optind > 1) {
if (*out_f == 0)
sprintf(omode, "w%s%c", detect_format(argv[optind+1]), level);
if (!(out = scram_open(argv[optind+1], omode))) {
fprintf(stderr, "Failed to open file %s\n", argv[optind+1]);
return 1;
}
} else {
if (!(out = scram_open("-", omode))) {
fprintf(stderr, "Failed to open file %s\n", argv[optind+1]);
return 1;
}
}
/* Set any format specific options */
scram_set_refs(out, refs = scram_get_refs(in));
scram_set_option(out, CRAM_OPT_VERBOSITY, verbose);
if (s_opt)
if (scram_set_option(out, CRAM_OPT_SEQS_PER_SLICE, s_opt))
return 1;
if (S_opt)
if (scram_set_option(out, CRAM_OPT_SLICES_PER_CONTAINER, S_opt))
return 1;
if (embed_ref)
if (scram_set_option(out, CRAM_OPT_EMBED_REF, embed_ref))
return 1;
if (use_bz2)
if (scram_set_option(out, CRAM_OPT_USE_BZIP2, use_bz2))
return 1;
if (use_arith)
if (scram_set_option(out, CRAM_OPT_USE_ARITH, use_arith))
return 1;
if (use_lzma)
if (scram_set_option(out, CRAM_OPT_USE_LZMA, use_lzma))
return 1;
if (binning != BINNING_NONE)
if (scram_set_option(out, CRAM_OPT_BINNING, binning))
return 1;
if (no_ref)
if (scram_set_option(out, CRAM_OPT_NO_REF, no_ref))
return 1;
if (multi_seq)
if (scram_set_option(out, CRAM_OPT_MULTI_SEQ_PER_SLICE, multi_seq))
return 1;
if (decode_md) {
if (no_ref) {
fprintf(stderr, "Cannot use -m in conjunction with -x.\n");
return 1;
}
if (scram_set_option(in, CRAM_OPT_DECODE_MD, decode_md))
return 1;
}
if (nthreads > 1) {
if (NULL == (p = t_pool_init(nthreads*2, nthreads)))
return 1;
if (scram_set_option(in, CRAM_OPT_THREAD_POOL, p))
return 1;
if (scram_set_option(out, CRAM_OPT_THREAD_POOL, p))
return 1;
}
if (ignore_md5)
if (scram_set_option(in, CRAM_OPT_IGNORE_MD5, ignore_md5))
return 1;
/* Copy header and refs from in to out, for writing purposes */
scram_set_header(out, scram_get_header(in));
// Needs doing after loading the header.
if (ref_fn) {
if (scram_set_option(out, CRAM_OPT_REFERENCE, ref_fn))
return 1;
} else {
// Attempt to fill out a cram->refs[] array from @SQ headers
scram_set_option(out, CRAM_OPT_REFERENCE, NULL);
}
if (scram_get_header(out)) {
char *arg_list = stringify_argv(argc, argv);
if (!arg_list)
return 1;
if (sam_hdr_add_PG(scram_get_header(out), "scramble",
"VN", PACKAGE_VERSION,
"CL", arg_list, NULL))
return 1;
if (scram_write_header(out))
return 1;
free(arg_list);
}
/* Support for sub-range queries, currently implemented for CRAM only */
if (*ref_name != 0) {
cram_range r;
int refid;
if (in->is_bam) {
fprintf(stderr, "Currently the -R option is only implemented for CRAM indices\n");
return 1;
}
cram_index_load(in->c, argv[optind]);
refid = sam_hdr_name2ref(in->c->header, ref_name);
if (refid == -1 && *ref_name != '*') {
fprintf(stderr, "Unknown reference name '%s'\n", ref_name);
return 1;
}
r.refid = refid;
r.start = start;
r.end = end;
if (scram_set_option(in, CRAM_OPT_RANGE, &r))
return 1;
}
/* Do the actual file format conversion */
s = NULL;
while (scram_get_seq(in, &s) >= 0) {
if (-1 == scram_put_seq(out, s)) {
fprintf(stderr, "Failed to encode sequence\n");
return 1;
}
if (max_reads >= 0)
if (--max_reads == 0)
break;
}
if (max_reads == -1) {
switch(scram_eof(in)) {
case 0:
fprintf(stderr, "Failed to decode sequence\n");
return 1;
case 2:
fprintf(stderr, "Warning: no end-of-file block identified. "
"File may be truncated.\n");
break;
case 1: default:
// expected case
break;
}
}
/* Finally tidy up and close files */
if (scram_close(in))
return 1;
if (scram_close(out))
return 1;
if (p)
t_pool_destroy(p, 0);
if (s)
free(s);
return 0;
}
int main(int argc, char **argv) {
cram_fd *out;
bam_file_t *in;
bam_seq_t *s = NULL;
char *out_fn;
int level = '\0'; // nul terminate string => auto level
char out_mode[4];
int c, verbose = 0;
int s_opt = 0, S_opt = 0, embed_ref = 0;
char *arg_list, *ref_fn = NULL;
while ((c = getopt(argc, argv, "u0123456789hvs:S:V:r:X")) != -1) {
switch (c) {
case '0': case '1': case '2': case '3': case '4':
case '5': case '6': case '7': case '8': case '9':
level = c;
break;
case 'u':
level = '0';
break;
case 'h':
usage(stdout);
return 0;
case 'v':
verbose++;
break;
case 's':
s_opt = atoi(optarg);
break;
case 'S':
S_opt = atoi(optarg);
break;
case 'V':
cram_set_option(NULL, CRAM_OPT_VERSION, optarg);
break;
case 'r':
ref_fn = optarg;
break;
case 'X':
embed_ref = 1;
break;
case '?':
fprintf(stderr, "Unrecognised option: -%c\n", optopt);
usage(stderr);
return 1;
}
}
if (argc - optind != 1 && argc - optind != 2) {
usage(stderr);
return 1;
}
/* opening */
if (NULL == (in = bam_open(argv[optind], "rb"))) {
perror(argv[optind]);
return 1;
}
out_fn = argc - optind == 2 ? argv[optind+1] : "-";
sprintf(out_mode, "wb%c", level);
if (NULL == (out = cram_open(out_fn, out_mode))) {
fprintf(stderr, "Error opening CRAM file '%s'.\n", out_fn);
return 1;
}
/* SAM Header */
if (!(arg_list = stringify_argv(argc, argv)))
return 1;
sam_hdr_add_PG(in->header, "sam_to_cram",
"VN", PACKAGE_VERSION,
"CL", arg_list, NULL);
free(arg_list);
/* Find and load reference */
if (!ref_fn) {
SAM_hdr_type *ty = sam_hdr_find(in->header, "SQ", NULL, NULL);
if (ty) {
SAM_hdr_tag *tag;
if ((tag = sam_hdr_find_key(in->header, ty, "UR", NULL))) {
ref_fn = tag->str + 3;
if (strncmp(ref_fn, "file:", 5) == 0)
ref_fn += 5;
}
}
}
out->header = in->header;
if (ref_fn)
cram_load_reference(out, ref_fn);
if (!out->refs) {
fprintf(stderr, "Unable to open reference.\n"
"Please specify a valid reference with -r ref.fa option.\n");
return 1;
}
refs2id(out->refs, out->header);
if (-1 == cram_write_SAM_hdr(out, in->header))
return 1;
cram_set_option(out, CRAM_OPT_VERBOSITY, verbose);
if (s_opt)
cram_set_option(out, CRAM_OPT_SEQS_PER_SLICE, s_opt);
if (S_opt)
cram_set_option(out, CRAM_OPT_SLICES_PER_CONTAINER, S_opt);
if (embed_ref)
cram_set_option(out, CRAM_OPT_EMBED_REF, embed_ref);
/* Sequence iterators */
while (bam_get_seq(in, &s) > 0) {
if (-1 == cram_put_bam_seq(out, s)) {
fprintf(stderr, "Failed in cram_put_bam_seq()\n");
return 1;
}
}
bam_close(in);
out->header = NULL; // freed by bam_close()
if (-1 == cram_close(out)) {
fprintf(stderr, "Failed in cram_close()\n");
return 1;
}
if (s)
free(s);
return 0;
}
/*
* Reads a version 3 CRAM file and replaces the header in-place,
* provided the header is small enough to fit without growing the
* entire file.
*
* Version 3 format has a SAM header held as an (optionally)
* compressed block within the header container. Additional
* uncompressed blocks or simply unallocated space (the difference
* between total block sizes and the container size) are used to
* provide room for growth or contraction of the compressed header.
*
* Returns 0 on success;
* -1 on general failure;
* -2 on failure due to insufficient size
*/
int cram_reheader_inplace3(cram_fd *fd, const bam_hdr_t *h, const char *arg_list,
int add_PG)
{
cram_container *c = NULL;
cram_block *b = NULL;
SAM_hdr *hdr = NULL;
off_t start, sz, end;
int container_sz, max_container_sz;
char *buf = NULL;
int ret = -1;
if (cram_major_vers(fd) < 2 ||
cram_major_vers(fd) > 3) {
fprintf(stderr, "[%s] unsupported CRAM version %d\n", __func__,
cram_major_vers(fd));
goto err;
}
if (!(hdr = sam_hdr_parse_(h->text, h->l_text)))
goto err;
if (add_PG && sam_hdr_add_PG(hdr, "samtools", "VN", samtools_version(),
arg_list ? "CL": NULL,
arg_list ? arg_list : NULL,
NULL))
goto err;
int header_len = sam_hdr_length(hdr);
/* Fix M5 strings? Maybe out of scope for this tool */
// Find current size of SAM header block
if ((start = hseek(cram_fd_get_fp(fd), 26, SEEK_SET)) != 26)
goto err;
if (!(c = cram_read_container(fd)))
goto err;
// +5 allows num_landmarks to increase from 0 to 1 (Cramtools)
max_container_sz = cram_container_size(c)+5;
sz = htell(cram_fd_get_fp(fd)) + cram_container_get_length(c) - start;
end = htell(cram_fd_get_fp(fd)) + cram_container_get_length(c);
// We force 1 block instead of (optionally) 2. C CRAM
// implementations for v3 were writing 1 compressed block followed
// by 1 uncompressed block. However this is tricky to deal with
// as changing block sizes can mean the block header also changes
// size due to itf8 and variable size integers.
//
// If we had 1 block, this doesn't change anything.
// If we had 2 blocks, the new container header will be smaller by
// 1+ bytes, requiring the cram_container_get_length(c) to be larger in value.
// However this is an int32 instead of itf8 so the container
// header structure stays the same size. This means we can always
// reduce the number of blocks without running into size problems.
cram_container_set_num_blocks(c, 1);
int32_t *landmark;
int32_t num_landmarks;
landmark = cram_container_get_landmarks(c, &num_landmarks);
if (num_landmarks && landmark) {
num_landmarks = 1;
landmark[0] = 0;
} else {
num_landmarks = 0;
}
cram_container_set_landmarks(c, num_landmarks, landmark);
buf = malloc(max_container_sz);
container_sz = max_container_sz;
if (cram_store_container(fd, c, buf, &container_sz) != 0)
goto err;
if (!buf)
goto err;
// Proposed new length, but changing cram_container_get_length(c) may change the
// container_sz and thus the remainder (cram_container_get_length(c) itself).
cram_container_set_length(c, sz - container_sz);
int old_container_sz = container_sz;
container_sz = max_container_sz;
if (cram_store_container(fd, c, buf, &container_sz) != 0)
goto err;
if (old_container_sz != container_sz) {
fprintf(stderr, "Quirk of fate makes this troublesome! "
"Please use non-inplace version.\n");
goto err;
}
// Version 3.0 supports compressed header
b = cram_new_block(FILE_HEADER, 0);
int32_put_blk(b, header_len);
cram_block_append(b, sam_hdr_str(hdr), header_len);
cram_block_update_size(b);
cram_compress_block(fd, b, NULL, -1, -1);
if (hseek(cram_fd_get_fp(fd), 26, SEEK_SET) != 26)
goto err;
if (cram_block_size(b) > cram_container_get_length(c)) {
fprintf(stderr, "New header will not fit. Use non-inplace version"
" (%d > %d)\n",
(int)cram_block_size(b), cram_container_get_length(c));
ret = -2;
goto err;
}
if (cram_write_container(fd, c) == -1)
goto err;
if (cram_write_block(fd, b) == -1)
goto err;
// Blank out the remainder
int rsz = end - htell(cram_fd_get_fp(fd));
assert(rsz >= 0);
if (rsz) {
char *rem = calloc(1, rsz);
ret = hwrite(cram_fd_get_fp(fd), rem, rsz) == rsz ? 0 : -1;
free(rem);
}
err:
if (c) cram_free_container(c);
if (buf) free(buf);
if (b) cram_free_block(b);
if (hdr) sam_hdr_free(hdr);
return ret;
}
/*
* Reads a version 2 CRAM file and replaces the header in-place,
* provided the header is small enough to fit without growing the
* entire file.
*
* Version 2 format has an uncompressed SAM header with multiple nul
* termination bytes to permit inline header editing.
*
* Returns 0 on success;
* -1 on general failure;
* -2 on failure due to insufficient size
*/
int cram_reheader_inplace2(cram_fd *fd, const bam_hdr_t *h, const char *arg_list,
int add_PG)
{
cram_container *c = NULL;
cram_block *b = NULL;
SAM_hdr *hdr = NULL;
off_t start;
int ret = -1;
if (cram_major_vers(fd) < 2 ||
cram_major_vers(fd) > 3) {
fprintf(stderr, "[%s] unsupported CRAM version %d\n", __func__,
cram_major_vers(fd));
goto err;
}
if (!(hdr = sam_hdr_parse_(h->text, h->l_text)))
goto err;
if (add_PG && sam_hdr_add_PG(hdr, "samtools", "VN", samtools_version(),
arg_list ? "CL": NULL,
arg_list ? arg_list : NULL,
NULL))
goto err;
int header_len = sam_hdr_length(hdr);
/* Fix M5 strings? Maybe out of scope for this tool */
// Load the existing header
if ((start = hseek(cram_fd_get_fp(fd), 26, SEEK_SET)) != 26)
goto err;
if (!(c = cram_read_container(fd)))
goto err;
// Version 2.1 has a single uncompressed block which is nul
// terminated with many nuls to permit growth.
//
// So load old block and keep all contents identical bar the
// header text itself
if (!(b = cram_read_block(fd)))
goto err;
if (cram_block_get_uncomp_size(b) < header_len+4) {
fprintf(stderr, "New header will not fit. Use non-inplace version (%d > %d)\n",
header_len+4, cram_block_get_uncomp_size(b));
ret = -2;
goto err;
}
cram_block_set_offset(b, 0); // rewind block
int32_put_blk(b, header_len);
cram_block_append(b, sam_hdr_str(hdr), header_len);
// Zero the remaining block
memset(cram_block_get_data(b)+cram_block_get_offset(b), 0,
cram_block_get_uncomp_size(b) - cram_block_get_offset(b));
// Make sure all sizes and byte-offsets are consistent after memset
cram_block_set_offset(b, cram_block_get_uncomp_size(b));
cram_block_set_comp_size(b, cram_block_get_uncomp_size(b));
if (hseek(cram_fd_get_fp(fd), start, SEEK_SET) != start)
goto err;
if (cram_write_container(fd, c) == -1)
goto err;
if (cram_write_block(fd, b) == -1)
goto err;
ret = 0;
err:
if (c) cram_free_container(c);
if (b) cram_free_block(b);
if (hdr) sam_hdr_free(hdr);
return ret;
}