view ezBAMQC/src/htslib/vcfutils.c @ 9:6610eedd9fae

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/*  vcfutils.c -- allele-related utility functions.

    Copyright (C) 2012-2014 Genome Research Ltd.

    Author: Petr Danecek <[e-mail]>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.  */

#include "htslib/vcfutils.h"

int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which)
{
    int i;
    for (i=0; i<line->n_allele; i++) ac[i]=0;

    // Use INFO/AC,AN field only when asked
    if ( which&BCF_UN_INFO )
    {
        bcf_unpack(line, BCF_UN_INFO);
        int an_id = bcf_hdr_id2int(header, BCF_DT_ID, "AN");
        int ac_id = bcf_hdr_id2int(header, BCF_DT_ID, "AC");
        int i, an=-1, ac_len=0, ac_type=0;
        uint8_t *ac_ptr=NULL;
        if ( an_id>=0 && ac_id>=0 )
        {
            for (i=0; i<line->n_info; i++)
            {
                bcf_info_t *z = &line->d.info[i];
                if ( z->key == an_id ) an = z->v1.i;
                else if ( z->key == ac_id ) { ac_ptr = z->vptr; ac_len = z->len; ac_type = z->type; }
            }
        }
        if ( an>=0 && ac_ptr )
        {
            int nac = 0;
            #define BRANCH_INT(type_t) {        \
                type_t *p = (type_t *) ac_ptr;  \
                for (i=0; i<ac_len; i++)        \
                {                               \
                    ac[i+1] = p[i];             \
                    nac += p[i];                \
                }                               \
            }
            switch (ac_type) {
                case BCF_BT_INT8:  BRANCH_INT(int8_t); break;
                case BCF_BT_INT16: BRANCH_INT(int16_t); break;
                case BCF_BT_INT32: BRANCH_INT(int32_t); break;
                default: fprintf(stderr, "[E::%s] todo: %d at %s:%d\n", __func__, ac_type, header->id[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break;
            }
            #undef BRANCH_INT
            if ( an<nac )
            {
                fprintf(stderr,"[E::%s] Incorrect AN/AC counts at %s:%d\n", __func__,header->id[BCF_DT_CTG][line->rid].key, line->pos+1); 
                exit(1); 
            }
            ac[0] = an - nac;
            return 1;
        }
    }

    // Split genotype fields only when asked
    if ( which&BCF_UN_FMT )
    {
        int i, gt_id = bcf_hdr_id2int(header,BCF_DT_ID,"GT");
        if ( gt_id<0 ) return 0;
        bcf_unpack(line, BCF_UN_FMT);
        bcf_fmt_t *fmt_gt = NULL;
        for (i=0; i<(int)line->n_fmt; i++)
            if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; }
        if ( !fmt_gt ) return 0;
        #define BRANCH_INT(type_t,vector_end) { \
            for (i=0; i<line->n_sample; i++) \
            { \
                type_t *p = (type_t*) (fmt_gt->p + i*fmt_gt->size); \
                int ial; \
                for (ial=0; ial<fmt_gt->n; ial++) \
                { \
                    if ( p[ial]==vector_end ) break; /* smaller ploidy */ \
                    if ( bcf_gt_is_missing(p[ial]) ) continue; /* missing allele */ \
                    if ( p[ial]>>1 > line->n_allele ) \
                    { \
                        fprintf(stderr,"[E::%s] Incorrect allele (\"%d\") in %s at %s:%d\n", __func__,(p[ial]>>1)-1, header->samples[i],header->id[BCF_DT_CTG][line->rid].key, line->pos+1); \
                        exit(1); \
                    } \
                    ac[(p[ial]>>1)-1]++; \
                } \
            } \
        }
        switch (fmt_gt->type) {
            case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_vector_end); break;
            case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
            case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
            default: fprintf(stderr, "[E::%s] todo: %d at %s:%d\n", __func__, fmt_gt->type, header->id[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break;
        }
        #undef BRANCH_INT
        return 1;
    }
    return 0;
}

int bcf_gt_type(bcf_fmt_t *fmt_ptr, int isample, int *_ial, int *_jal)
{
    int i, nals = 0, has_ref = 0, has_alt = 0, ial = 0, jal = 0;
    #define BRANCH_INT(type_t,vector_end) { \
        type_t *p = (type_t*) (fmt_ptr->p + isample*fmt_ptr->size); \
        for (i=0; i<fmt_ptr->n; i++) \
        { \
            if ( p[i] == vector_end ) break; /* smaller ploidy */ \
            if ( bcf_gt_is_missing(p[i]) ) continue; /* missing allele */ \
            int tmp = p[i]>>1; \
            if ( tmp>1 ) \
            { \
                if ( !ial ) { ial = tmp; has_alt = 1; } \
                else if ( tmp!=ial ) \
                { \
                    if ( tmp<ial ) \
                    { \
                        jal = ial; \
                        ial = tmp; \
                    } \
                    else \
                    { \
                        jal = tmp; \
                    } \
                    has_alt = 2; \
                } \
            } \
            else has_ref = 1; \
            nals++; \
        } \
    }
    switch (fmt_ptr->type) {
        case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_vector_end); break;
        case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
        case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
        default: fprintf(stderr, "[E::%s] todo: fmt_type %d\n", __func__, fmt_ptr->type); exit(1); break;
    }
    #undef BRANCH_INT

    if ( _ial ) *_ial = ial>0 ? ial-1 : ial;
    if ( _jal ) *_jal = jal>0 ? jal-1 : jal;
    if ( !nals ) return GT_UNKN;
    if ( nals==1 )
        return has_ref ? GT_HAPL_R : GT_HAPL_A;
    if ( !has_ref )
        return has_alt==1 ? GT_HOM_AA : GT_HET_AA;
    if ( !has_alt )
        return GT_HOM_RR;
    return GT_HET_RA;
}

int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line)
{
    int i;
    bcf_fmt_t *gt = bcf_get_fmt(header, line, "GT");
    if ( !gt ) return 0;

    int *ac = (int*) calloc(line->n_allele,sizeof(int));

    // check if all alleles are populated
    #define BRANCH(type_t,vector_end) { \
        for (i=0; i<line->n_sample; i++) \
        { \
            type_t *p = (type_t*) (gt->p + i*gt->size); \
            int ial; \
            for (ial=0; ial<gt->n; ial++) \
            { \
                if ( p[ial]==vector_end ) break; /* smaller ploidy */ \
                if ( bcf_gt_is_missing(p[ial]) ) continue; /* missing allele */ \
                if ( (p[ial]>>1)-1 >= line->n_allele ) { free(ac); return -1; } \
                ac[(p[ial]>>1)-1]++; \
            } \
        } \
    }
    switch (gt->type) {
        case BCF_BT_INT8:  BRANCH(int8_t,  bcf_int8_vector_end); break;
        case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_vector_end); break;
        case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_vector_end); break;
        default: fprintf(stderr, "[E::%s] todo: %d at %s:%d\n", __func__, gt->type, header->id[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break;
    }
    #undef BRANCH

    int rm_als = 0, nrm = 0;
    for (i=1; i<line->n_allele; i++)
    {
        if ( !ac[i] ) { rm_als |= 1<<i; nrm++; }
    }
    free(ac);

    if ( nrm ) bcf_remove_alleles(header, line, rm_als);
    return nrm;
}

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 ( bcf_gt_is_missing(ptr[j]) ) 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 inc = 0, nnew;
            if ( vlen==BCF_VL_A )
            {
                assert( nori==nA_ori );     // todo: will fail if all values are missing
                ndat = nA_new*line->n_sample;
                nnew = nA_new;
                inc  = 1;
            }
            else
            {
                assert( nori==nR_ori );     // todo: will fail if all values are missing
                ndat = nR_new*line->n_sample;
                nnew = nR_new;
            }

            #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*nnew; \
                    int size = sizeof(type_t); \
                    int k_src, k_dst = 0; \
                    for (k_src=0; k_src<nori; 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; \
                        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; \
                            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; \
                                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);
}