Пример #1
0
static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end)
{
    bam_hdr_t *hdr = conf->mplp_data[0]->h; // header of first file in input list

    int ret, i, tid, pos, ref_len;
    char *ref;

    while ( (ret=bam_mplp_auto(conf->iter, &tid, &pos, conf->n_plp, conf->plp)) > 0) 
    {
        if ( end && (pos<beg || pos>end) ) continue;
        if ( conf->bed && tid >= 0 )
        {
            int overlap = regidx_overlap(conf->bed, hdr->target_name[tid], pos, pos, NULL);
            if ( !conf->bed_logic ) overlap = overlap ? 0 : 1;
            if ( !overlap ) continue;
        }
        mplp_get_ref(conf->mplp_data[0], tid, &ref, &ref_len);

        int total_depth, _ref0, ref16;
        for (i = total_depth = 0; i < conf->nfiles; ++i) total_depth += conf->n_plp[i];
        group_smpl(conf->gplp, conf->bsmpl, conf->nfiles, conf->n_plp, conf->plp);
        _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
        ref16 = seq_nt16_table[_ref0];
        bcf_callaux_clean(conf->bca, &conf->bc);
        for (i = 0; i < conf->gplp->n; ++i)
            bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], ref16, conf->bca, conf->bcr + i);
        conf->bc.tid = tid; conf->bc.pos = pos;
        bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, ref16, &conf->bc);
        bcf_clear1(conf->bcf_rec);
        bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, 0, 0);
        flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);

        // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
        // check me: rghash in bcf_call_gap_prep() should have no effect, reads mplp_func already excludes them
        if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth 
            && bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref) >= 0)
        {
            bcf_callaux_clean(conf->bca, &conf->bc);
            for (i = 0; i < conf->gplp->n; ++i)
                bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i);
            if (bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, -1, &conf->bc) >= 0) 
            {
                bcf_clear1(conf->bcf_rec);
                bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref);
                flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);
            }
        }
    }
    return 0;
}
Пример #2
0
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_header_t *h = 0;
	char *ref;
	void *rghash = 0;

	bcf_callaux_t *bca = 0;
	bcf_callret1_t *bcr = 0;
	bcf_call_t bc;
	bcf_t *bp = 0;
	bcf_hdr_t *bh = 0;

	bam_sample_t *sm = 0;
	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(void*));
	plp = calloc(n, sizeof(void*));
	n_plp = calloc(n, sizeof(int*));
	sm = bam_smpl_init();

	// read the header and initialize data
	for (i = 0; i < n; ++i) {
		bam_header_t *h_tmp;
		data[i] = calloc(1, sizeof(mplp_aux_t));
		data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
		data[i]->conf = conf;
		h_tmp = bam_header_read(data[i]->fp);
		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);
		rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
		if (conf->reg) {
			int beg, end;
			bam_index_t *idx;
			idx = bam_index_load(fn[i]);
			if (idx == 0) {
				fprintf(stderr, "[%s] fail to load index for %d-th input.\n", __func__, i+1);
				exit(1);
			}
			if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) {
				fprintf(stderr, "[%s] malformatted region or wrong seqname for %d-th input.\n", __func__, i+1);
				exit(1);
			}
			if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
			data[i]->iter = bam_iter_query(idx, tid, beg, end);
			bam_index_destroy(idx);
		}
		if (i == 0) h = h_tmp;
		else {
			// FIXME: to check consistency
			bam_header_destroy(h_tmp);
		}
	}
	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(void*));

	fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
	// write the VCF header
	if (conf->flag & MPLP_GLF) {
		kstring_t s;
		bh = calloc(1, sizeof(bcf_hdr_t));
		s.l = s.m = 0; s.s = 0;
		bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w");
		for (i = 0; i < h->n_targets; ++i) {
			kputs(h->target_name[i], &s);
			kputc('\0', &s);
		}
		bh->l_nm = s.l;
		bh->name = malloc(s.l);
		memcpy(bh->name, s.s, s.l);
		s.l = 0;
		for (i = 0; i < sm->n; ++i) {
			kputs(sm->smpl[i], &s); kputc('\0', &s);
		}
		bh->l_smpl = s.l;
		bh->sname = malloc(s.l);
		memcpy(bh->sname, s.s, s.l);
		bh->txt = malloc(strlen(BAM_VERSION) + 64);
		bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION);
		free(s.s);
		bcf_hdr_sync(bh);
		bcf_hdr_write(bp, bh);
		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;
	}
	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;
	iter = bam_mplp_init(n, mplp_func, (void**)data);
	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);
	while (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_GLF) {
			int total_depth, _ref0, ref16;
			bcf1_t *b = calloc(1, sizeof(bcf1_t));
			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 = bam_nt16_table[_ref0];
			for (i = 0; i < gplp.n; ++i)
				bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
			bcf_call_combine(gplp.n, bcr, ref16, &bc);
			bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
						 (conf->flag&MPLP_FMT_SP), 0, 0);
			bcf_write(bp, bh, b);
			bcf_destroy(b);
			// call indels
			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) {
				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, -1, &bc) >= 0) {
					b = calloc(1, sizeof(bcf1_t));
					bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
								 (conf->flag&MPLP_FMT_SP), bca, ref);
					bcf_write(bp, bh, b);
					bcf_destroy(b);
				}
			}
		} else {
			printf("%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;
				printf("\t%d\t", n_plp[i]);
				if (n_plp[i] == 0) {
					printf("*\t*"); // FIXME: printf() is very slow...
					if (conf->flag & MPLP_PRINT_POS) printf("\t*");
				} else {
					for (j = 0; j < n_plp[i]; ++j)
						pileup_seq(plp[i] + j, pos, ref_len, ref);
					putchar('\t');
					for (j = 0; j < n_plp[i]; ++j) {
						const bam_pileup1_t *p = plp[i] + j;
						int c = bam1_qual(p->b)[p->qpos] + 33;
						if (c > 126) c = 126;
						putchar(c);
					}
					if (conf->flag & MPLP_PRINT_MAPQ) {
						putchar('\t');
						for (j = 0; j < n_plp[i]; ++j) {
							int c = plp[i][j].b->core.qual + 33;
							if (c > 126) c = 126;
							putchar(c);
						}
					}
					if (conf->flag & MPLP_PRINT_POS) {
						putchar('\t');
						for (j = 0; j < n_plp[i]; ++j) {
							if (j > 0) putchar(',');
							printf("%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
						}
					}
				}
			}
			putchar('\n');
		}
	}

	bcf_close(bp);
	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);
	bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr);
	bam_mplp_destroy(iter);
	bam_header_destroy(h);
	for (i = 0; i < n; ++i) {
		bam_close(data[i]->fp);
		if (data[i]->iter) bam_iter_destroy(data[i]->iter);
		free(data[i]);
	}
	free(data); free(plp); free(ref); free(n_plp);
	return 0;
}
Пример #3
0
/*
 * 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;
}
Пример #4
0
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_header_t *h = 0;
	char *ref;
	void *rghash = 0;

	bcf_callaux_t *bca = 0;
	bcf_callret1_t *bcr = 0;
	bcf_call_t bc;
	bcf_t *bp = 0;
	bcf_hdr_t *bh = 0;

	bam_sample_t *sm = 0;
	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(void*));
	plp = calloc(n, sizeof(void*));
	n_plp = calloc(n, sizeof(int*));
	sm = bam_smpl_init();

	// read the header and initialize data
	for (i = 0; i < n; ++i) {
		bam_header_t *h_tmp;
		data[i] = calloc(1, sizeof(mplp_aux_t));
		data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
		data[i]->conf = conf;
		h_tmp = bam_header_read(data[i]->fp);
		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);
		rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
		if (conf->reg) {
			int beg, end;
			bam_index_t *idx;
			idx = bam_index_load(fn[i]);
			if (idx == 0) {
				fprintf(stderr, "[%s] fail to load index for %d-th input.\n", __func__, i+1);
				exit(1);
			}
			if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) {
				fprintf(stderr, "[%s] malformatted region or wrong seqname for %d-th input.\n", __func__, i+1);
				exit(1);
			}
			if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
			data[i]->iter = bam_iter_query(idx, tid, beg, end);
			bam_index_destroy(idx);
		}
		if (i == 0) h = h_tmp;
		else {
			// FIXME: to check consistency
			bam_header_destroy(h_tmp);
		}
	}
	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(void*));

	fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
	// write the VCF header
	if (conf->flag & MPLP_GLF) {
		kstring_t s;
		bh = calloc(1, sizeof(bcf_hdr_t));
		s.l = s.m = 0; s.s = 0;
		bp = bcf_open("-", (conf->flag&MPLP_NO_COMP)? "wu" : "w");
		for (i = 0; i < h->n_targets; ++i) {
			kputs(h->target_name[i], &s);
			kputc('\0', &s);
		}
		bh->l_nm = s.l;
		bh->name = malloc(s.l);
		memcpy(bh->name, s.s, s.l);
		s.l = 0;
		for (i = 0; i < sm->n; ++i) {
			kputs(sm->smpl[i], &s); kputc('\0', &s);
		}
		bh->l_smpl = s.l;
		bh->sname = malloc(s.l);
		memcpy(bh->sname, s.s, s.l);
		bh->txt = malloc(strlen(BAM_VERSION) + 64);
		bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION);
		free(s.s);
		bcf_hdr_sync(bh);
		bcf_hdr_write(bp, bh);
		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;
	}
	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;
	iter = bam_mplp_init(n, mplp_func, (void**)data);
	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);


	int storeSize = 100;

	int delStore[2][100] = {{0},{0}};

	typedef char * mstring;

	while (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_GLF) {
			int total_depth, _ref0, ref16;
			bcf1_t *b = calloc(1, sizeof(bcf1_t));
			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 = bam_nt16_table[_ref0];
			for (i = 0; i < gplp.n; ++i)
				bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
			bcf_call_combine(gplp.n, bcr, ref16, &bc);
			bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
						 (conf->flag&MPLP_FMT_SP), 0, 0);
			bcf_write(bp, bh, b);
			bcf_destroy(b);
			// call indels
			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) {
				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, -1, &bc) >= 0) {
					b = calloc(1, sizeof(bcf1_t));
					bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
								 (conf->flag&MPLP_FMT_SP), bca, ref);
					bcf_write(bp, bh, b);
					bcf_destroy(b);
				}
			}
		} else {
			printf("%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;
				printf("\t%d\t", n_plp[i]);
				if (n_plp[i] == 0) {
					printf("*\t*"); // FIXME: printf() is very slow...
					if (conf->flag & MPLP_PRINT_POS) printf("\t*");
				} else {
					//MDW start					
					//for each position in the pileup column
					int charLen = 16;
					int countChars[ charLen ][2];
					int countiChars[ charLen ][2];

					int countGap[2]={0,0};

					//double qvTotal=0;
					int numStruck=0;
					int numGood=0;
					int tti;
					int ttj;
					mstring insAllele[100];
					int insAlleleCnt[100];
					int sf=0;
					int flag=0;

					//typedef char * string;
					char insStr0[10000];
					int iCnt0=0;

					char insStr1[10000];
					int iCnt1=0;

					char delStr0[10000];
					int dCnt0=0;

					char delStr1[10000];
					int dCnt1=0;


					float qposP[10000];
					int qposCnt=0;



					//initialize with zeros
						for(tti=0;tti<charLen;tti++){
						  countChars[tti][0]=0;
						  countChars[tti][1]=0;
						}

					// define repeat length here; look back up to 10 prior positions
					// start one position away.
					int replC=0; //
					for(tti=1;tti<=15;tti++){
						// check for greater than zero
						if(toupper(ref[pos-1])==toupper(ref[pos-tti])){
							replC++;
						}else{ // breaks the chain at first non identical to current position not strict homopolymer
							break;
						}
					}					
					int reprC=0; // 
					for(tti=1;tti<=15;tti++){
						// check for greater than zero
						if(toupper(ref[pos+1])==toupper(ref[pos+tti])){
							reprC++;
						}else{ // breaks the chain at first non identical to current position not strict homopolymer
							break;
						}
					}		
					int repT = replC;
					if(replC < reprC){
						repT=reprC;
					}



					for (j = 0; j < n_plp[i]; ++j){
						const bam_pileup1_t *p = plp[i] + j;
									
						/*
						SAME LOGIC AS pileup_seq()
						*/

						if(p->is_refskip){ // never count intron gaps in numStruck
							continue;
						}

						if(p->is_del){ // skip deletion gap, after first position which is the first aligned char
							continue;
						}

						if( 	p->b->core.qual < conf->min_mqToCount  || // mapping quality
							conf->maxrepC < (repT) || // max homopolymer run, this will not 
							(!p->is_del && bam1_qual(p->b)[p->qpos] < conf->min_baseQ) || // base quality for matches
							p->alignedQPosBeg <= (conf->trimEnd ) || p->alignedQPosEnd <= (conf->trimEnd ) ||  // trimEnd is 1-based
							p->zf == 1 || // fusion tag
							p->ih > conf->maxIH  || // max hit index
							(p->nmd > conf->maxNM) || // max mismatch
							(conf->flagFilter == 1 && !(p->b->core.flag&BAM_FPROPER_PAIR)) || // optionally keep only proper pairs
							(conf->flagFilter == 2 && p->b->core.flag&BAM_FSECONDARY) || // optionally strike secondary
							(conf->flagFilter == 3 && p->b->core.flag&BAM_FDUP) || // optionally strike dup
							(conf->flagFilter == 4 && (p->b->core.flag&BAM_FDUP || p->b->core.flag&BAM_FSECONDARY))  || // optionally strike secondary or dup
							(conf->flagFilter == 5 && (p->b->core.flag&BAM_FDUP || p->b->core.flag&BAM_FSECONDARY || p->b->core.flag&BAM_FQCFAIL || !(p->b->core.flag&BAM_FPROPER_PAIR) ))   // optionally strike secondary, dup and QCfail


						){
							numStruck++;
							continue;
						}

						
						//printf("repT=%d: %d %c %c %c %c \n",repT,p->indel,ref[pos],ref[pos-1],ref[pos-2],ref[pos-3]);


						if(!p->is_del && p->indel==0){
  						  countChars[ bam1_seqi(bam1_seq(p->b), p->qpos) ][ bam1_strand(p->b) ] ++;
						  numGood++;			

						}else if(p->is_refskip){
						  countGap[ bam1_strand(p->b) ]++;
						}
						
						if(p->indel<0){
    						  numGood++;			
						  if(bam1_strand(p->b) ==0){
							  for(tti=1;tti<= -p->indel; tti++) {
							    // current spot, starting at 0 in store, because indel<0 refers to next position
							   delStr0[dCnt0] =  ref[pos+tti];
							   dCnt0++;
							  }	
							  delStr0[dCnt0] = ',';
							  dCnt0++;
						  }else{
							  for(tti=1;tti<= -p->indel; tti++) {
							    // current spot, starting at 0 in store, because indel<0 refers to next position
							   delStr1[dCnt1] = ref[pos+tti];
							   dCnt1++;
							  }	
							  delStr1[dCnt1] = ',';
							  dCnt1++;
						  }



						}else if(p->indel>0){
						  numGood++;			

						  if(bam1_strand(p->b) ==0){
							  for(tti=1;tti<= p->indel; tti++) {
							    // current spot, starting at 0 in store, because indel<0 refers to next position
							   insStr0[iCnt0] = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + tti)];
							   iCnt0++;
							  }	
							  insStr0[iCnt0] = ',';
							  iCnt0++;
						  }else{
							  for(tti=1;tti<= p->indel; tti++) {
							    // current spot, starting at 0 in store, because indel<0 refers to next position
							   insStr1[iCnt1] = bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos + tti)];
							   iCnt1++;
							  }	
							  insStr1[iCnt1] = ',';
							  iCnt1++;
						  }


						}
						//calculate position of variant within aligned read - no soft clips
						if( toupper(ref[pos]) != toupper(bam_nt16_rev_table[bam1_seqi(bam1_seq(p->b), p->qpos)]) || p->indel>0 || p->indel<0  ){

						//distance to end; calculate distance to end of aligned read.  removes soft clips.
						int distToEnd = (p->alignedQPosBeg < p->alignedQPosEnd) ? p->alignedQPosBeg : p->alignedQPosEnd;
						qposP[qposCnt] = distToEnd;						  
						qposCnt++;	
						// printf("id=%s, pos=%d",bam1_qname(p->b),distToEnd);
						}	
					}

					//

					//print A,C,G,T, by +/-
				        printf("\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d", 	countChars[1][0],countChars[1][1],
											countChars[2][0],countChars[2][1],
											countChars[4][0],countChars[4][1],
											countChars[8][0],countChars[8][1],
											countChars[7][0],countChars[7][1]);
					
					putchar('\t');
					for(tti=0;tti<dCnt0;tti++){
					  putchar(delStr0[tti]);
					}

					putchar('\t');
					for(tti=0;tti<dCnt1;tti++){
					  putchar(delStr1[tti]);
					}

					putchar('\t');
					for(tti=0;tti<iCnt0;tti++){
					  putchar(insStr0[tti]);
					}

					putchar('\t');
					for(tti=0;tti<iCnt1;tti++){
					  putchar(insStr1[tti]);
					}

					printf("\t%d\t%d",numGood,numStruck);					

					// get non-ref qpos variation

					float medqpos = -1;
					float medAbsDev = -1;
					if(qposCnt>0){
					  medqpos = median(qposCnt,qposP);
					  float absDev[qposCnt];
					  for(tti=0;tti<qposCnt;tti++){
						absDev[tti] = abs(medqpos - qposP[tti]);
					  }
					  medAbsDev = median(qposCnt-1,absDev);
					}
					printf("\t%f",medAbsDev);

					///END MDW
				}



			}
			putchar('\n');
		}
	}

	bcf_close(bp);
	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);
	bcf_hdr_destroy(bh); bcf_call_destroy(bca); free(bc.PL); free(bcr);
	bam_mplp_destroy(iter);
	bam_header_destroy(h);
	for (i = 0; i < n; ++i) {
		bam_close(data[i]->fp);
		if (data[i]->iter) bam_iter_destroy(data[i]->iter);
		free(data[i]);
	}
	free(data); free(plp); free(ref); free(n_plp);
	return 0;
}