/*
* 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;
}
/*
* CRAM files don't store the RG:Z:ID per read in the aux field.
* Instead they have a numerical data series (RG) to point each read
* back to the Nth @RG line in the file. This means that we may need
* to edit the RG data series (if the files were produced from
* "samtools split" for example).
*
* The encoding method is stored in the compression header. Typical
* examples:
*
* RG => EXTERNAL {18} # Block content-id 18 holds RG values
* # as a series of ITF8 encoded values
*
* RG => HUFFMAN {1, 255, 255, 255, 255, 255, 1, 0}
* # One RG value #-1. (No RG)
*
* RG => HUFFMAN {1, 0, 1, 0} # One RG value #0 (always first RG)
*
* RG => HUFFMAN {2, 0, 1, 2, 1, 1}
* # Two RG values, #0 and #1, written
* # to the CORE block and possibly
* # mixed with other data series.
*
* A single value can (but may not be) implemented as a zero bit
* huffman code. In this situation we can change the meta-data in the
* compression header to renumber an RG value..
*/
int cram_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outcram)
{
samFile *out;
cram_fd *out_c;
int i, vers_maj, vers_min;
khash_s2i *rg2id = NULL;
bam_hdr_t *new_h = NULL;
/* Check consistent versioning and compatible headers */
if (!(new_h = cram_cat_check_hdr(nfn, fn, h, &rg2id, &vers_maj, &vers_min)))
return -1;
/* Open the file with cram_vers */
char vers[100];
sprintf(vers, "%d.%d", vers_maj, vers_min);
out = sam_open(outcram, "wc");
if (out == 0) {
fprintf(stderr, "[%s] ERROR: fail to open output file '%s'.\n", __func__, outcram);
return 1;
}
out_c = out->fp.cram;
cram_set_option(out_c, CRAM_OPT_VERSION, vers);
//fprintf(stderr, "Creating cram vers %s\n", vers);
cram_fd_set_header(out_c, sam_hdr_parse_(new_h->text, new_h->l_text)); // needed?
sam_hdr_write(out, new_h);
for (i = 0; i < nfn; ++i) {
samFile *in;
cram_fd *in_c;
cram_container *c;
bam_hdr_t *old;
int new_rg = -1;
in = sam_open(fn[i], "rc");
if (in == 0) {
fprintf(stderr, "[%s] ERROR: fail to open file '%s'.\n", __func__, fn[i]);
return -1;
}
in_c = in->fp.cram;
old = sam_hdr_read(in);
khash_s2i *rg2id_in = hash_rg(old);
// Compute RG mapping if suitable for changing.
if (rg2id_in->n_id == 1) {
int _;
new_rg = hash_s2i_inc(rg2id, rg2id_in->id[0], NULL, &_);
} else {
new_rg = 0;
}
hash_s2i_free(rg2id_in);
// Copy contains and blocks within them
while ((c = cram_read_container(in_c))) {
cram_block *blk;
if (cram_container_is_empty(in_c)) {
if (cram_write_container(out_c, c) != 0)
return -1;
// Container compression header
if (!(blk = cram_read_block(in_c)))
return -1;
if (cram_write_block(out_c, blk) != 0) {
cram_free_block(blk);
return -1;
}
cram_free_block(blk);
cram_free_container(c);
continue;
}
// If we have just one RG key and new_rg != 0 then
// we need to edit the compression header. IF WE CAN.
if (new_rg) {
int zero = 0;
//fprintf(stderr, "Transcode RG %d to %d\n", 0, new_rg);
cram_transcode_rg(in_c, out_c, c, 1, &zero, &new_rg);
} else {
int32_t num_slices;
// Not switching rg so do the usual read/write loop
if (cram_write_container(out_c, c) != 0)
return -1;
// Container compression header
if (!(blk = cram_read_block(in_c)))
return -1;
if (cram_write_block(out_c, blk) != 0) {
cram_free_block(blk);
return -1;
}
cram_free_block(blk);
// Container num_blocks can be invalid, due to a bug.
// Instead we iterate in slice context instead.
(void)cram_container_get_landmarks(c, &num_slices);
cram_copy_slice(in_c, out_c, num_slices);
}
cram_free_container(c);
}
bam_hdr_destroy(old);
sam_close(in);
}
sam_close(out);
hash_s2i_free(rg2id);
bam_hdr_destroy(new_h);
return 0;
}
