static void usage(FILE *fp)
{
/* Please improve the grouping */
fprintf(fp,
"\n"
"Program: samtools (Tools for alignments in the SAM format)\n"
"Version: %s (using htslib %s)\n\n", samtools_version(), hts_version());
fprintf(fp,
"Usage: samtools <command> [options]\n"
"\n"
"Commands:\n"
" -- Indexing\n"
" dict create a sequence dictionary file\n"
" faidx index/extract FASTA\n"
" index index alignment\n"
"\n"
" -- Editing\n"
" calmd recalculate MD/NM tags and '=' bases\n"
" fixmate fix mate information\n"
" reheader replace BAM header\n"
" rmdup remove PCR duplicates\n"
" targetcut cut fosmid regions (for fosmid pool only)\n"
" addreplacerg adds or replaces RG tags\n"
"\n"
" -- File operations\n"
" collate shuffle and group alignments by name\n"
" cat concatenate BAMs\n"
" merge merge sorted alignments\n"
" mpileup multi-way pileup\n"
" sort sort alignment file\n"
" split splits a file by read group\n"
" quickcheck quickly check if SAM/BAM/CRAM file appears intact\n"
" fastq converts a BAM to a FASTQ\n"
" fasta converts a BAM to a FASTA\n"
"\n"
" -- Statistics\n"
" bedcov read depth per BED region\n"
" depth compute the depth\n"
" flagstat simple stats\n"
" idxstats BAM index stats\n"
" phase phase heterozygotes\n"
" stats generate stats (former bamcheck)\n"
"\n"
" -- Viewing\n"
" flags explain BAM flags\n"
" tview text alignment viewer\n"
" view SAM<->BAM<->CRAM conversion\n"
" depad convert padded BAM to unpadded BAM\n"
"\n");
#ifdef _WIN32
fprintf(fp,
"Note: The Windows version of SAMtools is mainly designed for read-only\n"
" operations, such as viewing the alignments and generating the pileup.\n"
" Binary files generated by the Windows version may be buggy.\n\n");
#endif
}
/*
* 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 samtools_main(int argc, char *argv[])
{
#ifdef _WIN32
setmode(fileno(stdout), O_BINARY);
setmode(fileno(stdin), O_BINARY);
#endif
if (argc < 2) { usage(pysamerr); return 1; }
if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0) {
if (argc == 2) { usage(stdout); return 0; }
// Otherwise change "samtools help COMMAND [...]" to "samtools COMMAND";
// main_xyz() functions by convention display the subcommand's usage
// when invoked without any arguments.
argv++;
argc = 2;
}
int ret = 0;
if (strcmp(argv[1], "view") == 0) ret = main_samview(argc-1, argv+1);
else if (strcmp(argv[1], "import") == 0) ret = main_import(argc-1, argv+1);
else if (strcmp(argv[1], "mpileup") == 0) ret = bam_mpileup(argc-1, argv+1);
else if (strcmp(argv[1], "merge") == 0) ret = bam_merge(argc-1, argv+1);
else if (strcmp(argv[1], "sort") == 0) ret = bam_sort(argc-1, argv+1);
else if (strcmp(argv[1], "index") == 0) ret = bam_index(argc-1, argv+1);
else if (strcmp(argv[1], "idxstats") == 0) ret = bam_idxstats(argc-1, argv+1);
else if (strcmp(argv[1], "faidx") == 0) ret = faidx_main(argc-1, argv+1);
else if (strcmp(argv[1], "dict") == 0) ret = dict_main(argc-1, argv+1);
else if (strcmp(argv[1], "fixmate") == 0) ret = bam_mating(argc-1, argv+1);
else if (strcmp(argv[1], "rmdup") == 0) ret = bam_rmdup(argc-1, argv+1);
else if (strcmp(argv[1], "flagstat") == 0) ret = bam_flagstat(argc-1, argv+1);
else if (strcmp(argv[1], "calmd") == 0) ret = bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "fillmd") == 0) ret = bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "reheader") == 0) ret = main_reheader(argc-1, argv+1);
else if (strcmp(argv[1], "cat") == 0) ret = main_cat(argc-1, argv+1);
else if (strcmp(argv[1], "targetcut") == 0) ret = main_cut_target(argc-1, argv+1);
else if (strcmp(argv[1], "phase") == 0) ret = main_phase(argc-1, argv+1);
else if (strcmp(argv[1], "depth") == 0) ret = main_depth(argc-1, argv+1);
else if (strcmp(argv[1], "bam2fq") == 0 ||
strcmp(argv[1], "fastq") == 0 ||
strcmp(argv[1], "fasta") == 0) ret = main_bam2fq(argc-1, argv+1);
else if (strcmp(argv[1], "pad2unpad") == 0) ret = main_pad2unpad(argc-1, argv+1);
else if (strcmp(argv[1], "depad") == 0) ret = main_pad2unpad(argc-1, argv+1);
else if (strcmp(argv[1], "bedcov") == 0) ret = main_bedcov(argc-1, argv+1);
else if (strcmp(argv[1], "bamshuf") == 0) ret = main_bamshuf(argc-1, argv+1);
else if (strcmp(argv[1], "collate") == 0) ret = main_bamshuf(argc-1, argv+1);
else if (strcmp(argv[1], "stats") == 0) ret = main_stats(argc-1, argv+1);
else if (strcmp(argv[1], "flags") == 0) ret = main_flags(argc-1, argv+1);
else if (strcmp(argv[1], "split") == 0) ret = main_split(argc-1, argv+1);
else if (strcmp(argv[1], "quickcheck") == 0) ret = main_quickcheck(argc-1, argv+1);
else if (strcmp(argv[1], "addreplacerg") == 0) ret = main_addreplacerg(argc-1, argv+1);
else if (strcmp(argv[1], "pileup") == 0) {
fprintf(pysamerr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
return 1;
}
else if (strcmp(argv[1], "tview") == 0) ret = bam_tview_main(argc-1, argv+1);
else if (strcmp(argv[1], "--version") == 0) {
printf(
"samtools %s\n"
"Using htslib %s\n"
"Copyright (C) 2015 Genome Research Ltd.\n",
samtools_version(), hts_version());
}
else if (strcmp(argv[1], "--version-only") == 0) {
printf("%s+htslib-%s\n", samtools_version(), hts_version());
}
else {
fprintf(pysamerr, "[main] unrecognized command '%s'\n", argv[1]);
return 1;
}
return ret;
}
/*
* Performs pileup
* @param conf configuration for this pileup
* @param n number of files specified in fn
* @param fn filenames
*/
static int mpileup(mplp_conf_t *conf, int n, char **fn)
{
extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
extern void bcf_call_del_rghash(void *rghash);
mplp_aux_t **data;
int i, tid, pos, *n_plp, tid0 = -1, beg0 = 0, end0 = 1u<<29, ref_len, ref_tid = -1, max_depth, max_indel_depth;
const bam_pileup1_t **plp;
bam_mplp_t iter;
bam_hdr_t *h = NULL; /* header of first file in input list */
char *ref;
void *rghash = NULL;
FILE *pileup_fp = NULL;
bcf_callaux_t *bca = NULL;
bcf_callret1_t *bcr = NULL;
bcf_call_t bc;
htsFile *bcf_fp = NULL;
bcf_hdr_t *bcf_hdr = NULL;
bam_sample_t *sm = NULL;
kstring_t buf;
mplp_pileup_t gplp;
memset(&gplp, 0, sizeof(mplp_pileup_t));
memset(&buf, 0, sizeof(kstring_t));
memset(&bc, 0, sizeof(bcf_call_t));
data = calloc(n, sizeof(mplp_aux_t*));
plp = calloc(n, sizeof(bam_pileup1_t*));
n_plp = calloc(n, sizeof(int));
sm = bam_smpl_init();
if (n == 0) {
fprintf(stderr,"[%s] no input file/data given\n", __func__);
exit(1);
}
// read the header of each file in the list and initialize data
for (i = 0; i < n; ++i) {
bam_hdr_t *h_tmp;
data[i] = calloc(1, sizeof(mplp_aux_t));
data[i]->fp = sam_open(fn[i], "rb");
if ( !data[i]->fp )
{
fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
exit(1);
}
hts_set_fai_filename(data[i]->fp, conf->fai_fname);
data[i]->conf = conf;
h_tmp = sam_hdr_read(data[i]->fp);
if ( !h_tmp ) {
fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
exit(1);
}
data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
// Collect read group IDs with PL (platform) listed in pl_list (note: fragile, strstr search)
rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
if (conf->reg) {
hts_idx_t *idx = sam_index_load(data[i]->fp, fn[i]);
if (idx == 0) {
fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
exit(1);
}
if ( (data[i]->iter=sam_itr_querys(idx, data[i]->h, conf->reg)) == 0) {
fprintf(stderr, "[E::%s] fail to parse region '%s'\n", __func__, conf->reg);
exit(1);
}
if (i == 0) tid0 = data[i]->iter->tid, beg0 = data[i]->iter->beg, end0 = data[i]->iter->end;
hts_idx_destroy(idx);
}
if (i == 0) h = h_tmp; /* save the header of first file in list */
else {
// FIXME: to check consistency
bam_hdr_destroy(h_tmp);
}
}
// allocate data storage proportionate to number of samples being studied sm->n
gplp.n = sm->n;
gplp.n_plp = calloc(sm->n, sizeof(int));
gplp.m_plp = calloc(sm->n, sizeof(int));
gplp.plp = calloc(sm->n, sizeof(bam_pileup1_t*));
fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
// write the VCF header
if (conf->flag & MPLP_BCF)
{
const char *mode;
if ( conf->flag & MPLP_VCF )
mode = (conf->flag&MPLP_NO_COMP)? "wu" : "wz"; // uncompressed VCF or compressed VCF
else
mode = (conf->flag&MPLP_NO_COMP)? "wub" : "wb"; // uncompressed BCF or compressed BCF
bcf_fp = bcf_open(conf->output_fname? conf->output_fname : "-", mode);
if (bcf_fp == NULL) {
fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno));
exit(1);
}
bcf_hdr = bcf_hdr_init("w");
kstring_t str = {0,0,0};
ksprintf(&str, "##samtoolsVersion=%s+htslib-%s\n",samtools_version(),hts_version());
bcf_hdr_append(bcf_hdr, str.s);
str.l = 0;
ksprintf(&str, "##samtoolsCommand=samtools mpileup");
for (i=1; i<conf->argc; i++) ksprintf(&str, " %s", conf->argv[i]);
kputc('\n', &str);
bcf_hdr_append(bcf_hdr, str.s);
if (conf->fai_fname)
{
str.l = 0;
ksprintf(&str, "##reference=file://%s\n", conf->fai_fname);
bcf_hdr_append(bcf_hdr, str.s);
}
// todo: use/write new BAM header manipulation routines, fill also UR, M5
for (i=0; i<h->n_targets; i++)
{
str.l = 0;
ksprintf(&str, "##contig=<ID=%s,length=%d>", h->target_name[i], h->target_len[i]);
bcf_hdr_append(bcf_hdr, str.s);
}
free(str.s);
bcf_hdr_append(bcf_hdr,"##ALT=<ID=X,Description=\"Represents allele(s) other than observed.\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
#if CDF_MWU_TESTS
bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
#endif
bcf_hdr_append(bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
bcf_hdr_append(bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
if ( conf->fmt_flag&B2B_FMT_DP )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
if ( conf->fmt_flag&B2B_FMT_DV )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
if ( conf->fmt_flag&B2B_FMT_DPR )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
if ( conf->fmt_flag&B2B_INFO_DPR )
bcf_hdr_append(bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
if ( conf->fmt_flag&B2B_FMT_DP4 )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
if ( conf->fmt_flag&B2B_FMT_SP )
bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
for (i=0; i<sm->n; i++)
bcf_hdr_add_sample(bcf_hdr, sm->smpl[i]);
bcf_hdr_add_sample(bcf_hdr, NULL);
bcf_hdr_write(bcf_fp, bcf_hdr);
bca = bcf_call_init(-1., conf->min_baseQ);
bcr = calloc(sm->n, sizeof(bcf_callret1_t));
bca->rghash = rghash;
bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
bca->min_frac = conf->min_frac;
bca->min_support = conf->min_support;
bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
bc.bcf_hdr = bcf_hdr;
bc.n = sm->n;
bc.PL = malloc(15 * sm->n * sizeof(*bc.PL));
if (conf->fmt_flag)
{
assert( sizeof(float)==sizeof(int32_t) );
bc.DP4 = malloc(sm->n * sizeof(int32_t) * 4);
bc.fmt_arr = malloc(sm->n * sizeof(float)); // all fmt_flag fields
if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR) )
{
// first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
bc.DPR = malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
for (i=0; i<sm->n; i++)
bcr[i].DPR = bc.DPR + (i+1)*B2B_MAX_ALLELES;
}
}
}
else {
pileup_fp = conf->output_fname? fopen(conf->output_fname, "w") : stdout;
if (pileup_fp == NULL) {
fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname, strerror(errno));
exit(1);
}
}
if (tid0 >= 0 && conf->fai) { // region is set
ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
ref_tid = tid0;
for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
} else ref_tid = -1, ref = 0;
// begin pileup
iter = bam_mplp_init(n, mplp_func, (void**)data);
if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(iter);
max_depth = conf->max_depth;
if (max_depth * sm->n > 1<<20)
fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__);
if (max_depth * sm->n < 8000) {
max_depth = 8000 / sm->n;
fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, max_depth);
}
max_indel_depth = conf->max_indel_depth * sm->n;
bam_mplp_set_maxcnt(iter, max_depth);
bcf1_t *bcf_rec = bcf_init1();
int ret;
while ( (ret=bam_mplp_auto(iter, &tid, &pos, n_plp, plp)) > 0) {
if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
if (tid != ref_tid) {
free(ref); ref = 0;
if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len);
for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
ref_tid = tid;
}
if (conf->flag & MPLP_BCF) {
int total_depth, _ref0, ref16;
for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
_ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
ref16 = seq_nt16_table[_ref0];
bcf_callaux_clean(bca, &bc);
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
bc.tid = tid; bc.pos = pos;
bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
bcf_clear1(bcf_rec);
bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0);
bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
// call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0)
{
bcf_callaux_clean(bca, &bc);
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
bcf_clear1(bcf_rec);
bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref);
bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
}
}
} else {
fprintf(pileup_fp, "%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
for (i = 0; i < n; ++i) {
int j, cnt;
for (j = cnt = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
if (bam_get_qual(p->b)[p->qpos] >= conf->min_baseQ) ++cnt;
}
fprintf(pileup_fp, "\t%d\t", cnt);
if (n_plp[i] == 0) {
fputs("*\t*", pileup_fp);
if (conf->flag & MPLP_PRINT_MAPQ) fputs("\t*", pileup_fp);
if (conf->flag & MPLP_PRINT_POS) fputs("\t*", pileup_fp);
} else {
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
if (bam_get_qual(p->b)[p->qpos] >= conf->min_baseQ)
pileup_seq(pileup_fp, plp[i] + j, pos, ref_len, ref);
}
putc('\t', pileup_fp);
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
int c = bam_get_qual(p->b)[p->qpos];
if (c >= conf->min_baseQ) {
c = c + 33 < 126? c + 33 : 126;
putc(c, pileup_fp);
}
}
if (conf->flag & MPLP_PRINT_MAPQ) {
putc('\t', pileup_fp);
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
int c = bam_get_qual(p->b)[p->qpos];
if ( c < conf->min_baseQ ) continue;
c = plp[i][j].b->core.qual + 33;
if (c > 126) c = 126;
putc(c, pileup_fp);
}
}
if (conf->flag & MPLP_PRINT_POS) {
putc('\t', pileup_fp);
for (j = 0; j < n_plp[i]; ++j) {
if (j > 0) putc(',', pileup_fp);
fprintf(pileup_fp, "%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
}
}
}
}
putc('\n', pileup_fp);
}
}
// clean up
free(bc.tmp.s);
bcf_destroy1(bcf_rec);
if (bcf_fp)
{
hts_close(bcf_fp);
bcf_hdr_destroy(bcf_hdr);
bcf_call_destroy(bca);
free(bc.PL);
free(bc.DP4);
free(bc.DPR);
free(bc.fmt_arr);
free(bcr);
}
if (pileup_fp && conf->output_fname) fclose(pileup_fp);
bam_smpl_destroy(sm); free(buf.s);
for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
bcf_call_del_rghash(rghash);
bam_mplp_destroy(iter);
bam_hdr_destroy(h);
for (i = 0; i < n; ++i) {
sam_close(data[i]->fp);
if (data[i]->iter) hts_itr_destroy(data[i]->iter);
free(data[i]);
}
free(data); free(plp); free(ref); free(n_plp);
return ret;
}
/*
* 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;
}
