pop_haplo.cpp

/** \file pop_haplo.cpp
 *  \brief Functions for calculating haplotype-based statistics
 *  \author Daniel Garrigan
 *  \version 0.3
*/

#include "pop_haplo.h"
#include "tables.h"

int main_haplo(int argc, char *argv[])
{
    int chr;                  //! chromosome identifier
    int beg;                  //! beginning coordinate for analysis
    int end;                  //! end coordinate for analysis
    int ref;                  //! ref
    long num_windows;         //! number of windows
    std::string msg;          //! string for error message
    bam_plbuf_t *buf;         //! pileup buffer
    haploData t;

    // parse the command line options
    std::string region = t.parseCommandLine(argc, argv);

    // check input BAM file for errors
    t.checkBAM();

    // initialize the sample data structure
    t.bam_smpl_init();

    // add samples
    t.bam_smpl_add();

    // initialize error model
    t.em = errmod_init(1.-0.83);

    // parse genomic region
    int k = bam_parse_region(t.h, region, &chr, &beg, &end);
    if (k < 0)
    {
        msg = "Bad genome coordinates: " + region;
        fatal_error(msg, __FILE__, __LINE__, 0);
    }

    // fetch reference sequence
    t.ref_base = faidx_fetch_seq(t.fai_file, t.h->target_name[chr], 0, 0x7fffffff, &(t.len));

    // calculate the number of windows
    if (t.flag & BAM_WINDOW)
        num_windows = ((end-beg)-1)/t.win_size;
    else
    {
        t.win_size = (end-beg);
        num_windows = 1;
    }

    // iterate through all windows along specified genomic region
    for (long cw=0; cw < num_windows; cw++)
    {
        // construct genome coordinate string
        std::string scaffold_name(t.h->target_name[chr]);
        std::ostringstream winc(scaffold_name);
        winc.seekp(0, std::ios::end);
        winc << ":" << beg+(cw*t.win_size)+1 << "-" << ((cw+1)*t.win_size)+(beg-1);
        std::string winCoord = winc.str();

        // initialize number of sites to zero
        t.num_sites = 0;

        // parse the BAM file and check if region is retrieved from the reference
        if (t.flag & BAM_WINDOW)
        {
            k = bam_parse_region(t.h, winCoord, &ref, &(t.beg), &(t.end));
            if (k < 0)
            {
                msg = "Bad window coordinates " + winCoord;
                fatal_error(msg, __FILE__, __LINE__, 0);
            }
        }
        else
        {
            ref = chr;
            t.beg = beg;
            t.end = end;
            if (ref < 0)
            {
                msg = "Bad scaffold name: " + region;
                fatal_error(msg, __FILE__, __LINE__, 0);
            }
        }

        // initialize diverge specific variables
        t.init_haplo();

        // create population assignments
        t.assign_pops();

        // initialize pileup
        buf = bam_plbuf_init(make_haplo, &t);

        // fetch region from bam file
        if ((bam_fetch(t.bam_in->x.bam, t.idx, ref, t.beg, t.end, buf, fetch_func)) < 0)
        {
            msg = "Failed to retrieve region " + region + " due to corrupted BAM index file";
            fatal_error(msg, __FILE__, __LINE__, 0);
        }

        // finalize pileup
        bam_plbuf_push(0, buf);

        // calculate haplotype-based statistics
        t.calc_haplo();

        // print results to stdout
        t.print_haplo(chr);

        // take out the garbage
        t.destroy_haplo();
        bam_plbuf_destroy(buf);
    }
    // end of window interation

    errmod_destroy(t.em);
    samclose(t.bam_in);
    bam_index_destroy(t.idx);
    t.bam_smpl_destroy();
    free(t.ref_base);

    return 0;
}

int make_haplo(unsigned int tid, unsigned int pos, int n, const bam_pileup1_t *pl, void *data)
{
    int i;
    int fq;
    unsigned long long sample_cov;
    unsigned long long *cb = NULL;
    haploData *t = NULL;

    // get control data structure
    t = (haploData*)data;

    // only consider sites located in designated region
    if ((t->beg <= (int)pos) && (t->end > (int)pos))
    {
        // allocate memory pileup data
        try
        {
            cb = new unsigned long long [t->sm->n]();
        }
        catch (std::bad_alloc& ba)
        {
            std::cerr << "bad_alloc caught: " << ba.what() << std::endl;
        }

        // call bases
        t->call_base(n, pl, cb);

        // resolve heterozygous sites
        if (!(t->flag & BAM_HETEROZYGOTE))
            clean_heterozygotes(t->sm->n, cb, (int)t->ref_base[pos], t->min_snpQ);

        // determine if site is segregating
        fq = segbase(t->sm->n, cb, t->ref_base[pos], t->min_snpQ);

        // determine how many samples pass the quality filters
        sample_cov = qfilter(t->sm->n, cb, t->min_rmsQ, t->min_depth, t->max_depth);

        for (i=0; i < t->sm->npops; i++)
            t->pop_sample_mask[i] = sample_cov & t->pop_mask[i];

        if (popcount64(sample_cov) == t->sm->n)
        {
            // calculate the site type
            t->types[t->num_sites] = t->cal_site_type(cb);

            if (fq > 0)
            {
                t->hap.pos[t->segsites] = pos;
                t->hap.ref[t->segsites] = bam_nt16_table[(int)t->ref_base[pos]];
                for (i=0; i < t->sm->n; i++)
                {
                    t->hap.rms[i][t->segsites] = (cb[i]>>(CHAR_BIT*6))&0xffff;
                    t->hap.snpq[i][t->segsites] = (cb[i]>>(CHAR_BIT*4))&0xffff;
                    t->hap.num_reads[i][t->segsites] = (cb[i]>>(CHAR_BIT*2))&0xffff;
                    t->hap.base[i][t->segsites] = bam_nt16_table[(int)iupac[(cb[i]>>CHAR_BIT)&0xff]];
                    if (cb[i]&0x2ULL)
                        t->hap.seq[i][t->segsites/64] |= 0x1ULL << t->segsites%64;
                }
                t->hap.idx[t->segsites] = t->num_sites;
                t->segsites++;
            }
            t->num_sites++;
        }

        // take out the garbage
        delete [] cb;
    }
    return 0;
}

void haploData::calc_haplo(void)
{
    calc_diff_matrix(*(this));
    haplo_func do_haplo[3] = {&haploData::calc_nhaps, &haploData::calc_ehhs, &haploData::calc_minDxy};
    (this->*do_haplo[output])();
}

void haploData::calc_nhaps(void)
{
    int i, j, k, f;
    int nelem;

    for (i=0; i < sm->npops; i++)
    {
        nelem = pop_nsmpl[i];
        if (nelem > 1)
        {
            std::vector<int> b;
            std::vector<int>::iterator it1;
            std::vector<int>::iterator it2;

            // initialize the haplotype identity vector
            for (j=0; j < sm->n; j++)
                if (CHECK_BIT(pop_mask[i], j))
                    b.push_back(j);

            // assign haplotype identifiers
            for (j=0, it1=b.begin(); j < nelem-1; j++, it1++)
            {
                it2 = b.begin();
                for (k=j+1, std::advance(it2, j+1); k < nelem; k++, it2++)
                    if ((diff_matrix[j][k] == 0) && (*it2 > *it1))
                        b.at(k)=j;
            }

            // count number of haplotypes and calculate haplotype diversity
            int ff = 0;
            double sh;
            for (j=0; j < (int)b.size(); j++)
            {
                if ((f = count(b.begin(), b.end(), j)) > 0)
                    ++nhaps[i];
                ff += f*f;
            }
            sh = (double)(ff)/(double)SQ(nelem);
            hdiv[i] = 1.0-((1.0-sh)*(double)(nelem/(nelem-1)));
        }
        else
        {
            nhaps[i] = 1;
            hdiv[i] = 1.0;
        }
    }
}

void haploData::calc_ehhs(void)
{
    int i, j;

    calc_nhaps();

    for (i=0; i < sm->npops; i++)
    {
        if (pop_nsmpl[i] < 4)
            ehhs[i] = std::numeric_limits<double>::quiet_NaN();
        else
        {
            unsigned short popf;
            unsigned long long pop_type;
            std::list<unsigned long long> pop_site;

            // make list container of all non-singleton partitions present in population i
            for (j=0; j < segsites; j++)
            {
                pop_type = types[hap.idx[j]] & pop_mask[i];
                popf = popcount64(pop_type);
                if ((popf > 1) && (popf < pop_nsmpl[i]-1))
                    pop_site.push_back(pop_type);
            }

            // count unique partitions
            int before;
            int after;
            int part_count = 0;
            int part_max_count = 0;
            unsigned long long part_type = 0;
            unsigned long long part_type_comp = 0;
            unsigned long long max_site = 0;
            double sh;
            std::list<unsigned long long> uniq(pop_site);
            std::list<unsigned long long>::iterator it;
            uniq.sort();
            uniq.unique();

            for (it=uniq.begin(); it != uniq.end(); it++)
            {
                part_type = *it;

                // find the complement of part_type
                for (j=0; j < sm->n; j++)
                    if (~CHECK_BIT(part_type, j) && CHECK_BIT(pop_mask[i], j))
                        part_type_comp |= 0x1ULL << j;
                before = static_cast<int>(pop_site.size());
                pop_site.remove(part_type);
                pop_site.remove(part_type_comp);
                after = static_cast<int>(pop_site.size());
                part_count = (before-after)+1;
                if (part_count > part_max_count)
                {
                    part_max_count = part_count;
                    max_site = part_type;
                }
            }

            // calculate site heterozygosity
            popf = popcount64(max_site);
            sh = (1.0-((double)(SQ(popf)+((pop_nsmpl[i]-popf)*(pop_nsmpl[i]-popf)))/SQ(pop_nsmpl[i])))*(double)(pop_nsmpl[i]/(pop_nsmpl[i]-1));

            // calculate site-specific extended haplotype homozygosity
            ehhs[i] = hdiv[i]/(1.0-sh);
        }
    }
}

void haploData::calc_minDxy(void)
{
    int i, j, v, w;
    int npops = sm->npops;
    int n = sm->n;

    for (i=0; i < npops; i++)
    {
        for (j=i; j < npops; j++)
        {
            if (i != j)
                minDxy[i*npops+(j-(i+1))] = std::numeric_limits<unsigned int>::max();
            for (v=0; v < n-1; v++)
            {
                for (w=v+1; w < n; w++)
                {
                    if (CHECK_BIT(pop_mask[i], v) && CHECK_BIT(pop_mask[j], w))
                    {
                        if (i == j)
                            piw[i] += (double)diff_matrix[v][w];
                        else
                        {
                            pib[i*npops+(j-(i+1))] += (double)diff_matrix[v][w];
                            minDxy[i*npops+(j-(i+1))] = minDxy[i*npops+(j-(i+1))] < diff_matrix[v][w] ? minDxy[i*npops+(j-(i+1))] : diff_matrix[v][w];
                        }
                    }
                }
            }
            if (i != j)
                pib[i*npops+(j-(i+1))] *= 1.0/(double)(pop_nsmpl[i]*pop_nsmpl[j]);
            else
            {
                piw[i] *= 2.0/(double)(pop_nsmpl[i]*(pop_nsmpl[i]-1));
                if (isnan(piw[i]))
                    piw[i] = 0.0;
            }
        }
    }
}

void haploData::print_haplo(int chr)
{
    int i, j;

    //print coordinate information and number of aligned sites
    std::cout << h->target_name[chr] << "\t" << beg+1 << "\t" << end+1 << "\t" << num_sites;

    switch(output)
    {
    case 0:
        for (i=0; i < sm->npops; i++)
        {
            if (num_sites >= min_sites)
            {
                std::cout << "\tK[" << sm->popul[i] << "]:\t" << nhaps[i];
                std::cout << "\tKdiv[" << sm->popul[i] << "]:";
                std::cout << "\t" << std::fixed << std::setprecision(5) << 1.0 - hdiv[i];
            }
            else
            {
                std::cout << "\tK[" << sm->popul[i] << "]:\t" << std::setw(7) << "NA";
                std::cout << "\tKdiv[" << sm->popul[i] << "]:\t" << std::setw(7) << "NA";
            }
        }
        break;
    case 1:
        for (i=0; i < sm->npops; i++)
        {
            if (num_sites >= min_sites)
            {
                if (isnan(ehhs[i]))
                    std::cout << "\tEHHS[" << sm->popul[i] << "]:\t" << std::setw(7) << "NA";
                else
                {
                    std::cout << "\tEHHS[" << sm->popul[i] << "]:";
                    std::cout << "\t" << std::fixed << std::setprecision(5) << ehhs[i];
                }
            }
            else
                std::cout << "\tEHHS[" << sm->popul[i] << "]:\t" << std::setw(7) << "NA";
        }
        break;
    case 2:
        for (i=0; i < sm->npops; i++)
        {
            if (num_sites >= min_sites)
            {
                std::cout << "\tpi[" << sm->popul[i] << "]:";
                std::cout << "\t" << std::fixed << std::setprecision(5) << piw[i];
            }
            else
                std::cout << "\tpi[" << sm->popul[i] << "]:\t" << std::setw(7) << "NA";
        }

        for (i=0; i < sm->npops-1; i++)
        {
            for (j=i+1; j < sm->npops; j++)
            {
                if (num_sites >= min_sites)
                {
                    std::cout << "\tdxy[" << sm->popul[i] << "-" << sm->popul[j] << "]:";
                    std::cout << "\t" << std::fixed << std::setprecision(5) << pib[i*sm->npops+(j-(i+1))];
                    std::cout << "\tmin[" << sm->popul[i] << "-" << sm->popul[j] << "]:";
                    std::cout << "\t" << minDxy[i*sm->npops+(j-(i+1))];
                }
                else
                {
                    std::cout << "\tdxy[" << sm->popul[i] << "-" << sm->popul[j] << "]:\t" << std::setw(7) << "NA";
                    std::cout << "\tmin[" << sm->popul[i] << "-" << sm->popul[j] << "]:\t" << std::setw(7) << "NA";
                }
            }
        }
        break;
    default:
        break;
    }
    std::cout << std::endl;
}

void calc_diff_matrix(haploData &h)
{
    int i, j, k;
    int n = h.sm->n;
    int segs = h.segsites;

    // calculate number of pairwise differences
    for (i=0; i < n-1; i++)
        for (j=i+1; j < n; j++)
        {
            for (k=0; k <= SEG_IDX(segs); k++)
                h.diff_matrix[j][i] += hamming_distance(h.hap.seq[i][k], h.hap.seq[j][k]);
            h.diff_matrix[i][j] = h.diff_matrix[j][i];
        }
}

std::string haploData::parseCommandLine(int argc, char *argv[])
{
#ifdef _MSC_VER
    struct _stat finfo;
#else
    struct stat finfo;
#endif
    std::vector<std::string> glob_opts;
    std::string msg;

    GetOpt::GetOpt_pp args(argc, argv);
    args >> GetOpt::Option('f', reffile);
    args >> GetOpt::Option('h', headfile);
    args >> GetOpt::Option('o', output);
    args >> GetOpt::Option('m', min_depth);
    args >> GetOpt::Option('x', max_depth);
    args >> GetOpt::Option('q', min_rmsQ);
    args >> GetOpt::Option('s', min_snpQ);
    args >> GetOpt::Option('a', min_mapQ);
    args >> GetOpt::Option('b', min_baseQ);
    args >> GetOpt::Option('k', min_sites);
    args >> GetOpt::Option('w', win_size);
    if (args >> GetOpt::OptionPresent('w'))
    {
        win_size *= 1000;
        flag |= BAM_WINDOW;
    }
    if (args >> GetOpt::OptionPresent('h'))
        flag |= BAM_HEADERIN;
    if (args >> GetOpt::OptionPresent('i'))
        flag |= BAM_ILLUMINA;
    args >> GetOpt::GlobalOption(glob_opts);

    // run some checks on the command line

    // check if output option is valid
    if ((output < 0) || (output > 2))
    {
        msg = "Not a valid output option";
        fatal_error(msg, __FILE__, __LINE__, &haploUsage);
    }

    // if no input BAM file is specified -- print usage and exit
    if (glob_opts.size() < 2)
    {
        msg = "Need to specify BAM file name";
        fatal_error(msg, __FILE__, __LINE__, &haploUsage);
    }
    else
        bamfile = glob_opts[0];

    // check if specified BAM file exists on disk
    if ((stat(bamfile.c_str(), &finfo)) != 0)
    {
        msg = "Specified input file: " + bamfile + " does not exist";
        switch(errno)
        {
        case ENOENT:
            std::cerr << "File not found" << std::endl;
            break;
        case EINVAL:
            std::cerr << "Invalid parameter to stat" << std::endl;
            break;
        default:
            std::cerr << "Unexpected error in stat" << std::endl;
            break;
        }
        fatal_error(msg, __FILE__, __LINE__, 0);
    }

    // check if fastA reference file is specified
    if (reffile.empty())
    {
        msg = "Need to specify fastA reference file";
        fatal_error(msg, __FILE__, __LINE__, &haploUsage);
    }

    // check is fastA reference file exists on disk
    if ((stat(reffile.c_str(), &finfo)) != 0)
    {
        switch(errno)
        {
        case ENOENT:
            std::cerr << "File not found" << std::endl;
            break;
        case EINVAL:
            std::cerr << "Invalid parameter to stat" << std::endl;
            break;
        default:
            std::cerr << "Unexpected error in stat" << std::endl;
            break;
        }
        msg = "Specified reference file: " + reffile + " does not exist";
        fatal_error(msg, __FILE__, __LINE__, 0);
    }

    //check if BAM header input file exists on disk
    if (flag & BAM_HEADERIN)
    {
        if ((stat(headfile.c_str(), &finfo)) != 0)
        {
            switch(errno)
            {
            case ENOENT:
                std::cerr << "File not found" << std::endl;
                break;
            case EINVAL:
                std::cerr << "Invalid parameter to stat" << std::endl;
                break;
            default:
                std::cerr << "Unexpected error in stat" << std::endl;
                break;
            }
            msg = "Specified header file: " + headfile + " does not exist";
            fatal_error(msg, __FILE__, __LINE__, 0);
        }
    }

    // return the index of first non-optioned argument
    return glob_opts[1];
}

haploData::haploData(void)
{
    derived_type = HAPLO;
    output = 0;
    min_sites = 10;
    win_size = 0;
}

void haploData::init_haplo(void)
{
    int i;
    int length = end-beg;
    int n = sm->n;
    int npops = sm->npops;

    segsites = 0;

    try
    {
        types = new unsigned long long [length]();
        pop_mask = new unsigned long long [npops]();
        pop_nsmpl = new unsigned char [npops]();
        pop_sample_mask = new unsigned long long [npops]();
        nhaps = new int [npops]();
        hdiv = new double [npops]();
        piw = new double [npops]();
        pib = new double [npops*(npops-1)]();
        ehhs = new double [npops]();
        minDxy = new unsigned short [npops*(npops-1)]();
        hap.pos = new unsigned int [length]();
        hap.idx = new unsigned int [length]();
        hap.ref = new unsigned char [length]();
        hap.seq = new unsigned long long* [n];
        hap.base = new unsigned char* [n];
        hap.rms = new unsigned short* [n];
        hap.snpq = new unsigned short* [n];
        hap.num_reads = new unsigned short* [n];
        diff_matrix = new unsigned short* [n];
        for (i=0; i < n; i++)
        {
            hap.seq[i] = new unsigned long long [length]();
            hap.base[i] = new unsigned char [length]();
            hap.rms[i] = new unsigned short [length]();
            hap.snpq[i] = new unsigned short [length]();
            hap.num_reads[i] = new unsigned short [length]();
            diff_matrix[i] = new unsigned short [n]();
        }
    }
    catch (std::bad_alloc& ba)
    {
        std::cerr << "bad_alloc caught: " << ba.what() << std::endl;
    }
}

void haploData::destroy_haplo(void)
{
    int i;

    delete [] pop_mask;
    delete [] types;
    delete [] pop_nsmpl;
    delete [] pop_sample_mask;
    delete [] hdiv;
    delete [] nhaps;
    delete [] piw;
    delete [] pib;
    delete [] ehhs;
    delete [] minDxy;
    delete [] hap.pos;
    delete [] hap.idx;
    delete [] hap.ref;
    for (i=0; i < sm->n; i++)
    {
        delete [] hap.seq[i];
        delete [] hap.base[i];
        delete [] hap.num_reads[i];
        delete [] hap.snpq[i];
        delete [] hap.rms[i];
        delete [] diff_matrix[i];
    }
    delete [] hap.seq;
    delete [] hap.base;
    delete [] hap.snpq;
    delete [] hap.rms;
    delete [] hap.num_reads;
    delete [] diff_matrix;
}

void haploData::haploUsage(void)
{
    std::cerr << std::endl;
    std::cerr << "Usage:   popbam haplo [options] <in.bam> [region]" << std::endl;
    std::cerr << std::endl;
    std::cerr << "Options: -i          base qualities are Illumina 1.3+     [ default: Sanger ]" << std::endl;
    std::cerr << "         -h  FILE    Input header file                    [ default: none ]" << std::endl;
    std::cerr << "         -w  INT     use sliding window of size (kb)" << std::endl;
    std::cerr << "         -k  INT     minimum number of sites in window    [ default: 10 ]" << std::endl;
    std::cerr << "         -o  INT     analysis to output                   [ default: 0 ]" << std::endl;
    std::cerr << "                     0 : number of haplotypes" << std::endl;
    std::cerr << "                     1 : extended haplotype homozygosity statistic" << std::endl;
    std::cerr << "                     2 : minimum Dxy statistic" << std::endl;
    std::cerr << "         -f  FILE    Reference fastA file" << std::endl;
    std::cerr << "         -m  INT     minimum read coverage                [ default: 3 ]" << std::endl;
    std::cerr << "         -x  INT     maximum read coverage                [ default: 255 ]" << std::endl;
    std::cerr << "         -q  INT     minimum rms mapping quality          [ default: 25 ]" << std::endl;
    std::cerr << "         -s  INT     minimum snp quality                  [ default: 25 ]" << std::endl;
    std::cerr << "         -a  INT     minimum map quality                  [ default: 13 ]" << std::endl;
    std::cerr << "         -b  INT     minimum base quality                 [ default: 13 ]" << std::endl;
    std::cerr << std::endl;
    exit(EXIT_FAILURE);
}