예제 #1
0
파일: dosage.c 프로젝트: kgururaj/bcftools
int calc_dosage_GL(bcf1_t *rec)
{
    int i, j, nret = bcf_get_format_values(in_hdr,rec,"GL",(void**)&buf,&nbuf,pl_type);
    if ( nret<0 ) return -1;

    nret /= rec->n_sample;
    #define BRANCH(type_t,is_missing,is_vector_end) \
    { \
        type_t *ptr = (type_t*) buf; \
        for (i=0; i<rec->n_sample; i++) \
        { \
            float vals[3] = {0,0,0}; \
            for (j=0; j<nret; j++) \
            { \
                if ( is_missing || is_vector_end ) break; \
                vals[j] = exp(ptr[j]); \
            } \
            float sum = vals[0] + vals[1] + vals[2]; \
            printf("\t%.1f", sum==0 ? -1 : (vals[1] + 2*vals[2]) / sum); \
            ptr  += nret; \
        } \
    }
    switch (pl_type)
    {
        case BCF_HT_INT:  BRANCH(int32_t,ptr[j]==bcf_int32_missing,ptr[j]==bcf_int32_vector_end); break;
        case BCF_HT_REAL: BRANCH(float,bcf_float_is_missing(ptr[j]),bcf_float_is_vector_end(ptr[j])); break;
    }
    #undef BRANCH
    return 0;
}
예제 #2
0
bcf1_t *process(bcf1_t *rec)
{
    int nval = 0, i, j, nret = bcf_get_format_values(in_hdr,rec,"GP",(void**)&buf,&nbuf,gp_type);
    if ( nret<0 )
    {
        if (!nskip_gp) fprintf(stderr, "[impute-info.c] Warning: info tag not added to sites without GP tag\n");
        nskip_gp++;
        return rec; // require FORMAT/GP tag, return site unchanged
    }

    nret /= rec->n_sample;
    if ( nret != 3 )
    {
        if (!nskip_dip) fprintf(stderr, "[impute-info.c] Warning: info tag not added to sites that are not biallelic diploid\n");
        nskip_dip++;
        return rec; // require biallelic diploid, return site unchanged
    }

    double esum = 0, e2sum = 0, fsum = 0;
    #define BRANCH(type_t,is_missing,is_vector_end) \
    { \
        type_t *ptr = (type_t*) buf; \
        for (i=0; i<rec->n_sample; i++) \
        { \
            double vals[3] = {0,0,0}; \
            for (j=0; j<nret; j++) \
            { \
                if ( is_missing || is_vector_end ) break; \
                vals[j] = ptr[j]; \
            } \
            esum  += vals[1] + 2*vals[2]; \
            e2sum += (vals[1] + 2*vals[2]) * (vals[1] + 2*vals[2]); \
            fsum  += vals[1] + 4*vals[2]; \
            ptr   += nret; \
            nval++; \
        } \
    }
    switch (gp_type)
    {
        case BCF_HT_INT:  BRANCH(int32_t,ptr[j]==bcf_int32_missing,ptr[j]==bcf_int32_vector_end); break;
        case BCF_HT_REAL: BRANCH(float,bcf_float_is_missing(ptr[j]),bcf_float_is_vector_end(ptr[j])); break;
    }
    #undef BRANCH

    double theta = esum / (2 * (double)nval);
    float info  = (theta>0 && theta<1) ? (float)(1 - (fsum - e2sum) / (2 * (double)nval * theta * (1.0 - theta))) : 1;

    bcf_update_info_float(out_hdr, rec, "INFO", &info, 1);
    nrec++;
    return rec;
}
예제 #3
0
파일: vcfutils.c 프로젝트: NVlabs/nvbio
void bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int rm_mask)
{
    int *map = (int*) calloc(line->n_allele, sizeof(int));

    // create map of indexes from old to new ALT numbering and modify ALT
    kstring_t str = {0,0,0};
    kputs(line->d.allele[0], &str);

    int nrm = 0, i,j;  // i: ori alleles, j: new alleles
    for (i=1, j=1; i<line->n_allele; i++) 
    {
        if ( rm_mask & 1<<i )
        {
            // remove this allele
            line->d.allele[i] = NULL;
            nrm++;
            continue;
        }
        kputc(',', &str);
        kputs(line->d.allele[i], &str);
        map[i] = j;
        j++;
    }
    if ( !nrm ) { free(map); free(str.s); return; }

    int nR_ori = line->n_allele;
    int nR_new = line->n_allele-nrm;
    assert(nR_new > 0); // should not be able to remove reference allele
    int nA_ori = nR_ori-1;
    int nA_new = nR_new-1;

    int nG_ori = nR_ori*(nR_ori + 1)/2;
    int nG_new = nR_new*(nR_new + 1)/2;

    bcf_update_alleles_str(header, line, str.s);

    // remove from Number=G, Number=R and Number=A INFO fields.
    uint8_t *dat = NULL;
    int mdat = 0, ndat = 0, mdat_bytes = 0, nret;
    for (i=0; i<line->n_info; i++)
    {
        bcf_info_t *info = &line->d.info[i];
        int vlen = bcf_hdr_id2length(header,BCF_HL_INFO,info->key);
        
        if ( vlen!=BCF_VL_A && vlen!=BCF_VL_G && vlen!=BCF_VL_R ) continue; // no need to change

        int type = bcf_hdr_id2type(header,BCF_HL_INFO,info->key);
        if ( type==BCF_HT_FLAG ) continue;
        int size = 1;
        if ( type==BCF_HT_REAL || type==BCF_HT_INT ) size = 4;

        mdat = mdat_bytes / size;
        nret = bcf_get_info_values(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void**)&dat, &mdat, type);
        mdat_bytes = mdat * size;
        if ( nret<0 ) 
        { 
            fprintf(stderr,"[%s:%d %s] Could not access INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__, 
                bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret); 
            exit(1);
        }
        if ( type==BCF_HT_STR ) 
        { 
            str.l = 0;
            char *ss = (char*) dat, *se = (char*) dat;
            if ( vlen==BCF_VL_A || vlen==BCF_VL_R )
            {
                int nexp, inc = 0;
                if ( vlen==BCF_VL_A )
                {
                    nexp = nA_ori;
                    inc  = 1;
                }
                else
                    nexp = nR_ori;
                for (j=0; j<nexp; j++)
                {
                    if ( !*se ) break;
                    while ( *se && *se!=',' ) se++;
                    if ( rm_mask & 1<<(j+inc) ) 
                    { 
                        if ( *se ) se++;
                        ss = se; 
                        continue; 
                    }
                    if ( str.l ) kputc(',',&str);
                    kputsn(ss,se-ss,&str);
                    if ( *se ) se++;
                    ss = se;
                }
                assert( j==nexp );
            }
            else    // Number=G, assuming diploid genotype
            {
                int k = 0, n = 0;
                for (j=0; j<nR_ori; j++)
                {
                    for (k=0; k<=j; k++)
                    {
                        if ( !*se ) break;
                        while ( *se && *se!=',' ) se++;
                        n++;
                        if ( rm_mask & 1<<j || rm_mask & 1<<k ) 
                        { 
                            if ( *se ) se++;
                            ss = se; 
                            continue; 
                        }
                        if ( str.l ) kputc(',',&str);
                        kputsn(ss,se-ss,&str);
                        if ( *se ) se++;
                        ss = se;
                    }
                    if ( !*se ) break;
                }
                assert( n=nG_ori );
            }

            nret = bcf_update_info(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void*)str.s, str.l, type);
            if ( nret<0 )
            {
                fprintf(stderr,"[%s:%d %s] Could not update INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
                        bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret);
                exit(1);
            }
            continue; 
        }
        
        if ( vlen==BCF_VL_A || vlen==BCF_VL_R )
        {
            int inc = 0, ntop;
            if ( vlen==BCF_VL_A )
            {
                assert( nret==nA_ori );
                ntop = nA_ori;
                ndat = nA_new;
                inc  = 1;
            }
            else
            {
                assert( nret==nR_ori );
                ntop = nR_ori;
                ndat = nR_new;
            }
            int k = 0;

            #define BRANCH(type_t,is_vector_end) \
            { \
                type_t *ptr = (type_t*) dat; \
                int size = sizeof(type_t); \
                for (j=0; j<ntop; j++) /* j:ori, k:new */ \
                { \
                    if ( is_vector_end ) { memcpy(dat+k*size, dat+j*size, size); break; } \
                    if ( rm_mask & 1<<(j+inc) ) continue; \
                    if ( j!=k ) memcpy(dat+k*size, dat+j*size, size); \
                    k++; \
                } \
            }
            switch (type) 
            {
                case BCF_HT_INT:  BRANCH(int32_t,ptr[j]==bcf_int32_vector_end); break;
                case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr[j])); break;
            }
            #undef BRANCH
        }
        else    // Number=G
        {
            assert( nret==nG_ori );
            int k, l_ori = -1, l_new = 0;
            ndat = nG_new;

            #define BRANCH(type_t,is_vector_end) \
            { \
                type_t *ptr = (type_t*) dat; \
                int size = sizeof(type_t); \
                for (j=0; j<nR_ori; j++) \
                { \
                    for (k=0; k<=j; k++) \
                    { \
                        l_ori++; \
                        if ( is_vector_end ) { memcpy(dat+l_new*size, dat+l_ori*size, size); break; } \
                        if ( rm_mask & 1<<j || rm_mask & 1<<k ) continue; \
                        if ( l_ori!=l_new ) memcpy(dat+l_new*size, dat+l_ori*size, size); \
                        l_new++; \
                    } \
                } \
            }
            switch (type) 
            {
                case BCF_HT_INT:  BRANCH(int32_t,ptr[l_ori]==bcf_int32_vector_end); break;
                case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr[l_ori])); break;
            }
            #undef BRANCH
        }

        nret = bcf_update_info(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void*)dat, ndat, type);
        if ( nret<0 )
        {
            fprintf(stderr,"[%s:%d %s] Could not update INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
                    bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret);
            exit(1);
        }
    }

    // Update GT fields, the allele indexes might have changed
    for (i=1; i<line->n_allele; i++) if ( map[i]!=i ) break;
    if ( i<line->n_allele )
    {
        mdat = mdat_bytes / 4;  // sizeof(int32_t)
        nret = bcf_get_genotypes(header,line,(void**)&dat,&mdat);
        mdat_bytes = mdat * 4;
        if ( nret>0 )
        {
            nret /= line->n_sample;
            int32_t *ptr = (int32_t*) dat;
            for (i=0; i<line->n_sample; i++)
            {
                for (j=0; j<nret; j++)
                {
                    if ( ptr[j]==bcf_gt_missing ) continue;
                    if ( ptr[j]==bcf_int32_vector_end ) break;
                    int al = bcf_gt_allele(ptr[j]);
                    assert( al<nR_ori && map[al]>=0 );
                    ptr[j] = (map[al]+1)<<1 | (ptr[j]&1);
                }
                ptr += nret;
            }
            bcf_update_genotypes(header, line, (void*)dat, nret*line->n_sample);
        }
    }

    // Remove from Number=G, Number=R and Number=A FORMAT fields. 
    // Assuming haploid or diploid GTs
    for (i=0; i<line->n_fmt; i++)
    {
        bcf_fmt_t *fmt = &line->d.fmt[i];
        int vlen = bcf_hdr_id2length(header,BCF_HL_FMT,fmt->id);

        if ( vlen!=BCF_VL_A && vlen!=BCF_VL_G && vlen!=BCF_VL_R ) continue; // no need to change

        int type = bcf_hdr_id2type(header,BCF_HL_FMT,fmt->id);
        if ( type==BCF_HT_FLAG ) continue;

        int size = 1;
        if ( type==BCF_HT_REAL || type==BCF_HT_INT ) size = 4;

        mdat = mdat_bytes / size;
        nret = bcf_get_format_values(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void**)&dat, &mdat, type);
        mdat_bytes = mdat * size;
        if ( nret<0 ) 
        { 
            fprintf(stderr,"[%s:%d %s] Could not access FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__, 
                    bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret); 
            exit(1);
        }

        if ( type==BCF_HT_STR ) 
        {
            int size = nret/line->n_sample;     // number of bytes per sample
            str.l = 0;
            if ( vlen==BCF_VL_A || vlen==BCF_VL_R )
            {
                int nexp, inc = 0;
                if ( vlen==BCF_VL_A )
                {
                    nexp = nA_ori;
                    inc  = 1;
                }
                else
                    nexp = nR_ori;
                for (j=0; j<line->n_sample; j++)
                {
                    char *ss = ((char*)dat) + j*size, *se = ss + size, *ptr = ss;
                    int k_src = 0, k_dst = 0, l = str.l;
                    for (k_src=0; k_src<nexp; k_src++)
                    {
                        if ( ptr>=se || !*ptr) break;
                        while ( ptr<se && *ptr && *ptr!=',' ) ptr++;
                        if ( rm_mask & 1<<(k_src+inc) )
                        {
                            ss = ++ptr;
                            continue;
                        }
                        if ( k_dst ) kputc(',',&str);
                        kputsn(ss,ptr-ss,&str);
                        ss = ++ptr;
                        k_dst++;
                    }
                    assert( k_src==nexp );
                    l = str.l - l;
                    for (; l<size; l++) kputc(0, &str);
                }
            }
            else    // Number=G, diploid or haploid
            {
                for (j=0; j<line->n_sample; j++)
                {
                    char *ss = ((char*)dat) + j*size, *se = ss + size, *ptr = ss;
                    int k_src = 0, k_dst = 0, l = str.l;
                    int nexp = 0; // diploid or haploid?
                    while ( ptr<se )
                    {
                        if ( !*ptr ) break;
                        if ( *ptr==',' ) nexp++;
                        ptr++;
                    }
                    if ( ptr!=ss ) nexp++;
                    assert( nexp==nG_ori || nexp==nR_ori );
                    ptr = ss;
                    if ( nexp==nG_ori ) // diploid
                    {
                        int ia, ib;
                        for (ia=0; ia<nR_ori; ia++)
                        {
                            for (ib=0; ib<=ia; ib++)
                            {
                                if ( ptr>=se || !*ptr ) break;
                                while ( ptr<se && *ptr && *ptr!=',' ) ptr++;
                                if ( rm_mask & 1<<ia || rm_mask & 1<<ib )
                                {
                                    ss = ++ptr;
                                    continue;
                                }
                                if ( k_dst ) kputc(',',&str);
                                kputsn(ss,ptr-ss,&str);
                                ss = ++ptr;
                                k_dst++;
                            }
                            if ( ptr>=se || !*ptr ) break;
                        }
                    }
                    else    // haploid
                    {
                        for (k_src=0; k_src<nR_ori; k_src++)
                        {
                            if ( ptr>=se || !*ptr ) break;
                            while ( ptr<se && *ptr && *ptr!=',' ) ptr++;
                            if ( rm_mask & 1<<k_src )
                            {
                                ss = ++ptr;
                                continue;
                            }
                            if ( k_dst ) kputc(',',&str);
                            kputsn(ss,ptr-ss,&str);
                            ss = ++ptr;
                            k_dst++;
                        }
                        assert( k_src==nR_ori );
                        l = str.l - l;
                        for (; l<size; l++) kputc(0, &str);
                    }
                }
            }
            nret = bcf_update_format(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void*)str.s, str.l, type);
            if ( nret<0 )
            {
                fprintf(stderr,"[%s:%d %s] Could not update FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
                        bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret);
                exit(1);
            }
            continue;
        }

        int nori = nret / line->n_sample;
        if ( vlen==BCF_VL_A || vlen==BCF_VL_R || (vlen==BCF_VL_G && nori==nR_ori) ) // Number=A, R or haploid Number=G
        {
            int ntop, inc = 0;
            if ( vlen==BCF_VL_A )
            {
                assert( nori==nA_ori );     // todo: will fail if all values are missing
                ntop = nA_ori;
                ndat = nA_new*line->n_sample;
                inc  = 1;
            }
            else
            {
                assert( nori==nR_ori );     // todo: will fail if all values are missing
                ntop = nR_ori;
                ndat = nR_new*line->n_sample;
            }

            #define BRANCH(type_t,is_vector_end) \
            { \
                for (j=0; j<line->n_sample; j++) \
                { \
                    type_t *ptr_src = ((type_t*)dat) + j*nori; \
                    type_t *ptr_dst = ((type_t*)dat) + j*nA_new; \
                    int size = sizeof(type_t); \
                    int k_src, k_dst = 0; \
                    for (k_src=0; k_src<ntop; k_src++) \
                    { \
                        if ( is_vector_end ) { memcpy(ptr_dst+k_dst, ptr_src+k_src, size); break; } \
                        if ( rm_mask & 1<<(k_src+inc) ) continue; \
                        if ( k_src!=k_dst ) memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
                        k_dst++; \
                    } \
                } \
            }
            switch (type) 
            {
                case BCF_HT_INT:  BRANCH(int32_t,ptr_src[k_src]==bcf_int32_vector_end); break;
                case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr_src[k_src])); break;
            }
            #undef BRANCH
        }
        else    // Number=G, diploid or mixture of haploid+diploid
        {
            assert( nori==nG_ori );
            ndat = nG_new*line->n_sample;

            #define BRANCH(type_t,is_vector_end) \
            { \
                for (j=0; j<line->n_sample; j++) \
                { \
                    type_t *ptr_src = ((type_t*)dat) + j*nori; \
                    type_t *ptr_dst = ((type_t*)dat) + j*nG_new; \
                    int size = sizeof(type_t); \
                    int ia, ib, k_dst = 0, k_src; \
                    int nset = 0;   /* haploid or diploid? */ \
                    for (k_src=0; k_src<nG_ori; k_src++) { if ( is_vector_end ) break; nset++; } \
                    if ( nset==nR_ori ) /* haploid */ \
                    { \
                        for (k_src=0; k_src<nR_ori; k_src++) \
                        { \
                            if ( rm_mask & 1<<k_src ) continue; \
                            if ( k_src!=k_dst ) memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
                            k_dst++; \
                        } \
                        memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
                    } \
                    else /* diploid */ \
                    { \
                        k_src = -1; \
                        for (ia=0; ia<nR_ori; ia++) \
                        { \
                            for (ib=0; ib<=ia; ib++) \
                            { \
                                k_src++; \
                                if ( is_vector_end ) { memcpy(ptr_dst+k_dst, ptr_src+k_src, size); ia = nR_ori; break; } \
                                if ( rm_mask & 1<<ia || rm_mask & 1<<ib ) continue; \
                                if ( k_src!=k_dst ) memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
                                k_dst++; \
                            } \
                        } \
                    } \
                } \
            }
            switch (type) 
            {
                case BCF_HT_INT:  BRANCH(int32_t,ptr_src[k_src]==bcf_int32_vector_end); break;
                case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr_src[k_src])); break;
            }
            #undef BRANCH
        }
        nret = bcf_update_format(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void*)dat, ndat, type);
        if ( nret<0 )
        {
            fprintf(stderr,"[%s:%d %s] Could not update FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
                    bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret);
            exit(1);
        }
    }
    free(dat);
    free(str.s);
    free(map);
}