New upstream version 1.2.0

all: vcflib/Makefile log

	cd src && $(MAKE)

wbamtools: vcflib/Makefile log

	cd src && $(MAKE) -f Makefile.bamtools

log: src/version_git.h

	wget -q http://hypervolu.me/freebayes/build/$(shell cat src/version_git.h | grep v | cut -f 3 -d\  | sed s/\"//g) &

## Compilation

FreeBayes requires g++ and the standard C and C++ development libraries.

Additionally, cmake is required for building the BamTools API.

    make

    sudo make install

Note that the freebayes-parallel script and the programs on which it depends are

not installed by this command.

Users can optionally build with [BamTools](https://github.com/pezmaster31/bamtools) instead of [SeqLib](https://github.com/walaj/SeqLib). Building with BamTools requires CMake.

    make wbamtools

## Usage

scripts/freebayes-parallel script.  If you find freebayes to be slow, you

should probably be running it in parallel using this script to run on a single

host, or generating a series of scripts, one per region, and run them on a

cluster.

cluster. Be aware that the freebayes-parallel script contains calls to other programs  using relative paths from the scripts subdirectory; the easiest way to ensure a successful run is to invoke the freebayes-parallel script from within the scripts subdirectory.

## Calling variants: from fastq to VCF

determination of candidate polymorphic loci.  Once such loci are determined, 

haplotype observations are extracted from reads where:

1. putative variants lie within `--haplotype-window` bases of each other 

1. putative variants lie within `--haplotype-length` bases of each other 

(default 3bp),

2. the reference sequence has repeats (e.g. microsatellites or STRs are called 

as one haplotype),

of haplotypes, considering all other putative variants supported by the 

alignment to be sequencing errors:

    freebayes -f ref.fa --haplotype-window 500 \

    freebayes -f ref.fa --haplotype-length 500 \

        --haplotype-basis-alleles vars.vcf aln.bam >haps.vcf

These steps should allow us to read long haplotypes directly from input data 

completely different literal haplotype.  To a point, this property improves our 

signal to noise ratio and can effectively filter out sequencing errors at the 

point of the input filters, but it also decreases the effective observation 

depth will prevent the generation of any calls if a long `--haplotype-window` 

depth will prevent the generation of any calls if a long `--haplotype-length` 

is combined with high a sequencing error rate.

This is BibTeX, Version 0.99d (TeX Live 2015/dev/Debian)

This is BibTeX, Version 0.99d (TeX Live 2015/Debian)

Capacity: max_strings=35307, hash_size=35307, hash_prime=30011

The top-level auxiliary file: main.aux

The style file: genome_research.bst

            return quality;

            break;

    }

    return 0;

}

const long double Allele::lncurrentQuality(void) const {

    return out.str();

}

string json(vector<Allele*> &alleles) {

string tojson(vector<Allele*> &alleles) {

    stringstream out;

    vector<Allele*>::iterator a = alleles.begin();

    out << "[" << (*a)->json(); ++a;

    out << "[" << (*a)->tojson(); ++a;

    for (; a != alleles.end(); ++a)

        out << "," << (*a)->json();

        out << "," << (*a)->tojson();

    out << "]";

    return out.str();

}

string json(Allele*& allele) { return allele->json(); }

string tojson(Allele*& allele) { return allele->tojson(); }

string Allele::json(void) {

string Allele::tojson(void) {

    stringstream out;

    if (!genotypeAllele) {

        out << "{\"id\":\"" << readID << "\""

        case 'M':

        case 'X':

        case 'D':

        case 'N':

            r += c->first;

            break;

        case 'N':

        case 'I':

        default:

            break;

        case 'M':

        case 'X':

        case 'D':

        case 'N':

            r += c->first;

            break;

        case 'N':

        case 'I':

        default:

            break;

// combines the two alleles into a complex variant, updates important data

void Allele::mergeAllele(const Allele& newAllele, AlleleType newType) {

    //cout << stringForAllele(*this) << endl << stringForAllele(newAllele) << endl;

    //cerr << stringForAllele(*this) << endl << stringForAllele(newAllele) << endl;

    type = newType;

    alternateSequence += newAllele.alternateSequence;

    length += newAllele.length; // hmmm

    basesRight = newAllele.basesRight;

    baseQualities.insert(baseQualities.end(), newAllele.baseQualities.begin(), newAllele.baseQualities.end());

    currentBase = base();

    // XXX note that we don't add Q values for intermingled gaps in combined alleles

    if (newAllele.type != ALLELE_REFERENCE) {

        quality = min(newAllele.quality, quality);

        lnquality = max(newAllele.lnquality, lnquality);

        //quality = minQuality(baseQualities);

        //lnquality = log(quality);

    } else {

    quality = averageQuality(baseQualities);

        lnquality = log(quality);

    lnquality = phred2ln(quality);

    basesRight += newAllele.referenceLength;

    }

    if (newAllele.type != ALLELE_REFERENCE) {

        repeatRightBoundary = newAllele.repeatRightBoundary;

    }

    cigar = mergeCigar(cigar, newAllele.cigar);

    referenceLength = referenceLengthFromCigar();

    //cout << stringForAllele(*this) << endl << endl;

}

void Allele::squash(void) {

    friend ostream &operator<<(ostream &out, Allele &a);

    friend ostream &operator<<(ostream &out, Allele* &a);

    friend string json(vector<Allele*> &alleles, long int &position);

    friend string json(vector<Allele*> &alleles);

    friend string json(Allele &allele, long int &position);

    friend string json(Allele* &allele);

    friend string tojson(vector<Allele*> &alleles, long int &position);

    friend string tojson(vector<Allele*> &alleles);

    friend string tojson(Allele &allele, long int &position);

    friend string tojson(Allele* &allele);

public:

                                    //  this is used to update cached data in the allele prior to presenting the allele for analysis

                                    //  for the current base, just use allele.currentBase

    string json(void);

    string tojson(void);

    unsigned int getLengthOnReference(void);

    int referenceLengthFromCigar(void);