/**

VCFv4.2 (including BCF) reader and writer.

Specifications: https://samtools.github.io/hts-specs/VCFv4.2.pdf

*/
module dhtslib.vcf;

import core.stdc.string;
import core.vararg;

import std.conv: to, ConvException;
import std.datetime;
import std.format: format;
import std.range: ElementType;
import std.string: fromStringz, toStringz;
import std.traits: isArray, isDynamicArray, isBoolean, isIntegral, isFloatingPoint, isNumeric, isSomeString;
import std.traits: Unqual;

import dhtslib.htslib.hts_log;
import dhtslib.htslib.kstring;
import dhtslib.htslib.vcf;

alias BCFRecord = VCFRecord;
alias BCFWriter = VCFWriter;

/** Wrapper around bcf_hdr_t

    Q: Why do we have VCFHeader, but not SAMHeader?
    A: Most (all)? of the SAM (bam1_t) manipulation functions do not require a ptr to the header,
    whereas almost all of the VCF (bcf1_t) manipulation functions do. Therefore, we track bcf_hdr_t*
    inside each VCFRecord; this is wrapped by VCFHeader for future convenience (for example,
    now we have @property nsamples; may move the tag reader and writer functions here?)

    In order to avoid double free()'ing an instance bcf_hdr_t,
    this wrapper will be the authoritative holder of of bcf_hdr_t ptrs,
    it shall be passed around by reference, and copies are disabled.
*/
struct VCFHeader
{
    /// Pointer to htslib BCF/VCF header struct; will be freed from VCFHeader dtor 
    bcf_hdr_t *hdr;

    // Copies have to be disabled to avoid double free()
    @disable this(this);

    ~this()
    {
        // Deallocate header
        if (this.hdr != null) bcf_hdr_destroy(this.hdr);
    }

    invariant
    {
        assert(this.hdr != null);
    }

    /// List of contigs in the header
    @property string[] sequences()
    {
        import core.stdc.stdlib : free;
        int nseqs;

        /** Creates a list of sequence names. It is up to the caller to free the list (but not the sequence names) */
        //const(char) **bcf_hdr_seqnames(const(bcf_hdr_t) *h, int *nseqs);
        const(char) **ary = bcf_hdr_seqnames(this.hdr, &nseqs);
        if (!nseqs) return [];

        string[] ret;
        ret.reserve(nseqs);

        for(int i; i < nseqs; i++) {
            ret ~= fromStringz(ary[i]).idup;
        }

        free(ary);
        return ret;        
    }

    /// Number of samples in the header
    pragma(inline, true)
    @property int nsamples() { return bcf_hdr_nsamples(this.hdr); }

}

/** Wrapper around bcf1_t 

    Because it uses bcf1_t internally, it must conform to the BCF2 part
    of the VCFv4.2 specs, rather than the loosey-goosey VCF specs. i.e.,
    INFO, CONTIG, FILTER records must exist in the header.

    TODO: Does this need to be kept in a consistent state?
    Ideally, VCFWriter would reject invalid ones, but we are informed
    that it is invalid (e.g. if contig not found) while building this
    struct; bcf_write1 will actually segfault, unfortunately. I'd like
    to avoid expensive validate() calls for every record before writing
    if possible, which means keeping this consistent. However, not
    sure what to do if error occurs when using the setters herein?

    2019-01-23 struct->class to mirror SAMRecord -- faster if reference type?

    2019-01-23 WIP: getters for chrom, pos, id, ref, alt are complete (untested)

After parsing a BCF or VCF line, bcf1_t must be unpacked. (not applicable when building bcf1_t from scratch)
Depending on information needed, this can be done to various levels with performance tradeoff.
Unpacking symbols:
BCF_UN_ALL: all
BCF_UN_SHR: all shared information (BCF_UN_STR|BCF_UN_FLT|BCF_UN_INFO)

                        BCF_UN_STR
                       /               BCF_UN_FLT
                      |               /      BCF_UN_INFO
                      |              |      /       ____________________________ BCF_UN_FMT
                      V              V     V       /       |       |       |
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA00001 NA00002 NA00003 ...

*/
class VCFRecord
{
    bcf1_t* line;   /// htslib structured record TODO: change to 'b' for better internal consistency? (vcf.h/c actually use line quite a bit in fn params)

    VCFHeader *vcfheader;   /// corresponding header (required);
                            /// is ptr to avoid copying struct containing ptr to bcf_hdr_t (leads to double free())

    /** VCFRecord

    Construct a bcf/vcf record, backed by bcf1_t, from: an existing bcf1_t, parameters, or a VCF line.

    Internal backing by bcf1_t means it must conform to the BCF2 rules -- i.e., header must contain
    appropriate INFO, CONTIG, and FILTER lines.

    Protip: specifying alternate MAX_UNPACK can speed it tremendously
        as it will not unpack all fields, only up to those requested (see htslib.vcf)
        For example, BCF_UN_STR is up to ALT inclusive, and BCF_UN_STR is up to FILTER
    */
    this(T)(T *h, bcf1_t *b, int MAX_UNPACK = BCF_UN_ALL)
    if(is(T == VCFHeader) || is(T == bcf_hdr_t))
    {
        static if (is(T == VCFHeader)) this.vcfheader = h;
        //else static if (is(T == bcf_hdr_t)) this.vcfheader = new VCFHeader(h); // double free() bug if we don't own bcf_hdr_t h
        else static if (is(T == bcf_hdr_t)) assert(0);  // ferret out situations that will lead to free() crashes
        else assert(0);

        this.line = b;

        // Now it must be unpacked
        // Protip: specifying alternate MAX_UNPACK can speed it tremendously
        immutable int ret = bcf_unpack(this.line, MAX_UNPACK);    // unsure what to do c̄ return value // @suppress(dscanner.suspicious.unused_variable)
    }
    /// ditto
    this(SS)(VCFHeader *vcfhdr, string chrom, int pos, string id, string _ref, string alt, float qual, SS filter, )
    if (isSomeString!SS || is(SS == string[]))
    {
        this.line = bcf_init1();
        this.vcfheader = vcfhdr;
        
        this.chrom = chrom;
        this.pos = pos;
        this.id = id;

        this.setAlleles(_ref, alt);

        this.qual = qual;
        this.filter = filter;
    }
    /// ditto
    this(VCFHeader *vcfhdr, string line, int MAX_UNPACK = BCF_UN_ALL)
    {
        this.vcfheader = vcfhdr;

        kstring_t kline;
        auto dupline = line.dup; // slower, but safer than a cast // @suppress(dscanner.suspicious.unmodified)

        kline.l = dupline.length;
        kline.m = dupline.length;
        kline.s = dupline.ptr;

        this.line = bcf_init1();
        this.line.max_unpack = MAX_UNPACK;

        auto ret = vcf_parse(&kline, this.vcfheader.hdr, this.line);
        if (ret < 0) {
            hts_log_error(__FUNCTION__, "vcf_parse returned < 0 -- code error or malformed VCF line");
        } else {
            ret = bcf_unpack(this.line, MAX_UNPACK);    // unsure what to do c̄ return value
        }
    }

    /// disable copying to prevent double-free (which should not come up except when writeln'ing)
    //@disable this(this);  // commented out as class has no postblit ctor (relevant when VCFRecord was struct)
    /// dtor
    ~this()
    {
        if (this.line) bcf_destroy1(this.line);
    }

    //////// FIXED FIELDS ////////
    
    /* CHROM */
    /// Get chromosome (CHROM)
    @property
    string chrom()
    {
        if (!this.line.unpacked)
            bcf_unpack(this.line, BCF_UN_STR);
        
        return fromStringz(bcf_hdr_id2name(this.vcfheader.hdr, this.line.rid)).idup;
    }
    /// Set chromosome (CHROM)
    @property
    void chrom(const(char)[] c)
    {
        auto rid = bcf_hdr_name2id(this.vcfheader.hdr, toStringz(c));
        if (rid == -1) {
            hts_log_error(__FUNCTION__, format("contig not found: %s", c));
            throw new Exception("contig not found");
        }
        else line.rid = rid;
    }


    /* POS */
    /// Get position (POS)
    // NB: internally BCF is uzing 0 based coordinates; we only show +1 when printing a VCF line with toString (which calls vcf_format)
    @property
    int pos()
    out(coord) { assert(coord >= 0); }
    do
    {
        if (!this.line.unpacked) bcf_unpack(this.line, BCF_UN_STR);
        return this.line.pos;
    }
    /// Set position (POS)
    @property
    void pos(int p)
    in { assert(p >= 0); }
    do
    {
        // TODO: should we check for pos >= 0 && pos < contig length? Could really hamper performance.
        // TODO: if writing out the file with invalid POS values crashes htslib, will consider it
        this.line.pos = p;
    }


    /* ID */
    /// Get ID string
    @property string id()
    {
        if (!this.line.unpacked) bcf_unpack(this.line, BCF_UN_STR);
        return fromStringz(this.line.d.id).idup;
    }
    /// Sets new ID string; comma-separated list allowed but no dup checking performed
    @property int id(const(char)[] id)
    {
        // bcf_update_id expects null pointer instead of empty string to mean "no value"
        if (id == "") return bcf_update_id(this.vcfheader.hdr, this.line, null);
        else return bcf_update_id(this.vcfheader.hdr, this.line, toStringz(id));
    }
    /// Append an ID (htslib performs duplicate checking)
    int addID(const(char)[] id)
    {
        if(id == "") return 0;
        return bcf_add_id(this.vcfheader.hdr, this.line, toStringz(id));
    }


    /* Alleles (REF, ALT)
    
        Internally, alleles are stored as a \0 separated array:
        [C \0 T \0 T T \0.. \0]
         ^    ^    ^ ^
         |    |    L L ALT_1 = "TT"
         |    L ALT_0 
         L REF

        TODO: Getters and setters poorly or inconsistently (?) named at this time or there are too many overloads?
        TODO: need non-overwriting setter for ref and alt alleles
        TODO: some of these may be inefficent; since they may be used in hot inner loops, pls optimize
    */
    /// REF allele length
    @property int refLen()
    {
        version(DigitalMars) pragma(inline);
        version(LDC) pragma(inline, true);
        version(GNU) pragma(inline, true);
        return this.line.rlen;
    }
    /// All alleles getter (array)
    @property string[] allelesAsArray()
    {
        string[] ret;
        ret.length = this.line.n_allele;        // n=0, no reference; n=1, ref but no alt
        foreach(int i; 0 .. this.line.n_allele) // ref allele is index 0
        {
            ret[i] = fromStringz(this.line.d.allele[i]).idup;
        }
        return ret;
    }
    /// Reference allele getter
    @property string refAllele()
    {
        if (!this.line.unpacked) bcf_unpack(this.line, BCF_UN_STR);
        if (this.line.n_allele < 1) return ""; // a valid record could have no ref (or alt) alleles
        else return fromStringz(this.line.d.als).idup;
    }
    // NB WIP: there could be zero, or multiple alt alleles
    /+@property string altAlleles()
    {
        if (!this.line.unpacked) bcf_unpack(this.line, BCF_UN_STR);
        return fromStringz(this.line.d.als)
    }+/
    /// Alternate alleles getter version 1: ["A", "ACTG", ...]
    @property string[] altAllelesAsArray()
    {
        if (!this.line.unpacked) bcf_unpack(this.line, BCF_UN_STR);

        string[] ret;
        if (this.line.n_allele < 2) return ret; // n=0, no reference; n=1, ref but no alt
        return this.allelesAsArray[1 .. $];     // trim off REF
    }
    /// Alternate alleles getter version 2: "A,ACTG,..."
    @property string altAllelesAsString()
    {
        if (!this.line.unpacked) bcf_unpack(this.line, BCF_UN_STR);

        string ret;
        if (this.line.n_allele < 2) return ret; // n=0, no reference; n=1, ref but no alt

        char[] tmp;
        tmp.length = this.line.d.m_allele;    // max allocated size in htslib

        char *a = this.line.d.allele[1];    // ref allele is index 0
        const char *last = this.line.d.allele[this.line.n_allele - 1];    // pointer to start of last allele
        size_t i = 0;

        assert( this.line.d.allele[1] == (this.line.d.als + this.line.rlen + 1) );  // ensue data structure is as we think (+1: past ref's term \0)

        while (i < this.line.d.m_allele)    // safety stop at max allocated size
        {
            if (*a) tmp[i] = *a;
            else {  // '\0'
                if (a < last) tmp[i] = ',';
                else break;
            }
            i++;
            a++;
        }
        tmp.length = i;

        return tmp.idup;
    }
    /// Set alleles; comma-separated list
    @property void alleles(string a)
    {
        if (a == "") {
            this.line.n_allele = 0;
            if (this.line.d.m_allele) this.line.d.als[0] = '\0';    // if storage allocated, zero out the REF
        }
        else
            bcf_update_alleles_str(this.vcfheader.hdr, this.line, toStringz(a));
    }
    /// Set alleles; array
    @property void alleles(string[] a)
    {
        if (a.length == 0) {
            this.line.n_allele = 0;
            if (this.line.d.m_allele) this.line.d.als[0] = '\0';    // if storage allocated, zero out the REF
        }
        else {
            const(char)*[64] allelesp;  // will fail if a locus has more than 63 ALT alleles :-O
            foreach(i; 0 .. a.length ) {
                // In order to zero out all alleles, pass a zero-length allele to the string version,
                // or a zero-length array to this version. Zero length string member of nonempty allele array is an error.
                if (a[i].length == 0) {
                    hts_log_error(__FUNCTION__, "Zero-length allele in nonempty allele array. Setting to '.'");
                    allelesp[i] = ".".ptr;
                }
                else allelesp[i] = toStringz(a[i]);
            }
            bcf_update_alleles(this.vcfheader.hdr, this.line, &allelesp[0], cast(int)a.length);
        }
    }
    /// Set REF allele only
    /// param r is \0-term Cstring
    /// TODO: UNTESTED
    void setRefAllele(const(char)* r)
    {
        // first, get REF
        if (!this.line.unpacked) bcf_unpack(this.line, BCF_UN_STR);
        // a valid record could have no ref (or alt) alleles
        if (this.line.n_allele < 2) // if none or 1 (=REF only), just add the REF we receieved
            bcf_update_alleles(this.vcfheader.hdr, this.line, &r, 1);
        else {
            // length of REF allele is allele[1] - allele[0], (minus one more for \0)
            // TODO ** TODO ** : there is a property line.refLen already
            const auto reflen = (this.line.d.allele[1] - this.line.d.allele[0]) - 1;
            if (strlen(r) <= reflen) {
                memcpy(this.line.d.allele[0], r, reflen + 1);   // +1 -> copy a trailing \0 in case original REF was longer than new 
                // TODO: do we need to call _sync ?
            } else {
                // slower way: replace allele[0] with r, but keep rest of pointers poitning at existing allele block,
                // then call bcf_update_alleles; this will make complete new copy of this.line.d.allele, so forgive the casts
                this.line.d.allele[0] = cast(char*) r;
                bcf_update_alleles(this.vcfheader.hdr, this.line,
                    cast( const(char)** ) this.line.d.allele, this.line.n_allele);
            }
        }
    }
    /// Set alleles; alt can be comma separated
    void setAlleles(string _ref, string alt)
    {
        immutable string alleles = _ref ~ "," ~ alt ~ "\0";
        bcf_update_alleles_str(this.vcfheader.hdr, this.line, alleles.ptr);
    }
    /// Set alleles; min. 2 alleles (ref, alt1); unlimited alts may be specified
    void setAlleles(string _ref, string alt, ...)
    {
        string alleles = _ref ~ "," ~ alt;

        for (int i = 0; i < _arguments.length; i++)
        {
            alleles ~= "," ~ va_arg!string(_argptr);
        }

        alleles ~= "\0";

        bcf_update_alleles_str(this.vcfheader.hdr, this.line, alleles.ptr);
    }


    /* Quality (QUAL) */
    /// Get variant quality (QUAL)
    @property float qual()
    out(result) { assert(result >= 0); }
    do
    {
        if (this.line.max_unpack < BCF_UN_FLT) bcf_unpack(this.line, BCF_UN_FLT);
        return this.line.qual;
    }
    /// Set variant quality (QUAL)
    @property void qual(float q)
    in { assert(q >= 0); }
    do { this.line.qual = q; }


    /* FILTER */
    /// Get FILTER column (nothing in htslib sadly)
    @property string filter()
    {
        const(char)[] ret;

        if (this.line.max_unpack < BCF_UN_FLT) bcf_unpack(this.line, BCF_UN_FLT);

        if (this.line.d.n_flt) {
            for(int i; i< this.line.d.n_flt; i++) {
                if (i) ret ~= ";";
                ret ~= fromStringz(this.vcfheader.hdr.id[BCF_DT_ID][ this.line.d.flt[0] ].key);
            }
        } else {
            ret = ".";
        }

        return ret.idup;
    }
    /// Remove all entries in FILTER
    void removeAllFilters()
    {
        // always returns zero
        bcf_update_filter(this.vcfheader.hdr, this.line, null, 0);
    }
    /// Set the FILTER column to f
    @property void filter(string f)
    {
        this.filter([f]);
    }
    /// Set the FILTER column to f0,f1,f2...
    /// TODO: determine definitiely whether "." is replaced with "PASS"
    @property void filter(string[] fs)
    {
        int[] fids;
        foreach(f; fs) {
            if(f == "") continue;
            const int fid = bcf_hdr_id2int(this.vcfheader.hdr, BCF_DT_ID, toStringz(f));
            if (fid == -1) hts_log_warning(__FUNCTION__, format("filter not found in header (ignoring): %s", f) );
            else fids ~= fid;
        }
        if (fids.length > 0)
            bcf_update_filter(this.vcfheader.hdr, this.line, fids.ptr, cast(int)fids.length);
        else
            hts_log_warning(__FUNCTION__, "No FILTER update was performed due to empty list");
    }
    /// Add a filter; from htslib: 
    /// "If flt_id is PASS, all existing filters are removed first. If other than PASS, existing PASS is removed."
    int addFilter(string f)
    {
        return bcf_add_filter(this.vcfheader.hdr, this.line, 
            bcf_hdr_id2int(this.vcfheader.hdr, BCF_DT_ID, toStringz(f)));
    }
    /// Remove a filter by name
    int removeFilter(string f)
    {
        const int fid = bcf_hdr_id2int(this.vcfheader.hdr, BCF_DT_ID, toStringz(f));
        return removeFilter(fid);
    }
    /// Remove a filter by numeric id
    int removeFilter(int fid)
    {
        return bcf_remove_filter(this.vcfheader.hdr, this.line, fid, 0);
    }
    /// Determine whether FILTER is present. log warning if filter does not exist. "PASS" and "." can be used interchangeably.
    bool hasFilter(string filter)
    {
        char[] f = filter.dup ~ '\0';
        //const auto id = bcf_hdr_id2int(this.vcfheader.hdr, BCF_DT_ID, f.ptr);
        const auto ret = bcf_has_filter(this.vcfheader.hdr, this.line, f.ptr);

        if (ret > 0) return true;
        else if (ret == 0) return false;
        else {
            hts_log_warning(__FUNCTION__, format("FILTER %s does not exist in the header", filter));
            return false;
        }
    }


    /* INFO */
    /+
        int tmpi = 1;
        bcf_update_info_int32(this.vcfhdr.hdr, line, toStringz("NS"c), &tmpi, 1);
    +/
    /// Add a tag:value to the INFO column -- tag must already exist in the header
    void addInfo(T)(string tag, T data)
    {
        int ret = -1;

        static if(isIntegral!T) {
            auto integer = cast(int) data;
            ret = bcf_update_info_int32(this.vcfheader.hdr, this.line, toStringz(tag), &integer, 1);
        }
        
        else static if(isFloatingPoint!T) {
            auto flt = cast(float) data;    // simply passing "2.0" (or whatever) => data is a double
            ret = bcf_update_info_float(this.vcfheader.hdr, this.line, toStringz(tag), &flt, 1);
        }

        else static if(isSomeString!T)
            ret = bcf_update_info_string(this.vcfheader.hdr, this.line, toStringz(tag), toStringz(data));
        
        else static if(isBoolean!T) {
            immutable int set = data ? 1 : 0; // if data == true, pass 1 to bcf_update_info_flag(n=); n=0 => clear flag 
            ret = bcf_update_info_flag(this.vcfheader.hdr, this.line, toStringz(tag), null, set);
        }
        
        if (ret == -1)
            hts_log_warning(__FUNCTION__, format("Couldn't add tag (ignoring): %s with value %s", tag, data));
    }
    /// ditto
    /// This handles a vector of values for the tag
    void addInfo(T)(string tag, T[] data)
    if(!is(T==immutable(char)))             // otherwise string::immutable(char)[] will match the other template
    {
        int ret = -1;

        static if(isIntegral!T) {
            auto integer = cast(int) data;
            ret = bcf_update_info_int32(this.vcfheader.hdr, this.line, toStringz(tag), &integer, data.length);
        }
        
        else static if(isFloatingPoint!T) {
            auto flt = cast(float) data;    // simply passing "2.0" (or whatever) => data is a double
            ret = bcf_update_info_float(this.vcfheader.hdr, this.line, toStringz(tag), &flt, data.length);
        }
        
        if (ret == -1)
            hts_log_warning(__FUNCTION__, format("Couldn't add tag (ignoring): %s with value %s", tag, data));
    }

    /* FORMAT (sample info) */
    /// bc_update_format_{int32,flat,string,flag}
    void addFormat(T)(string tag, T data)
    if(!isArray!T)
    {
        int ret = -1;

        static if(isIntegral!T) {
            auto integer = cast(int) data;
            ret = bcf_update_format_int32(this.vcfheader.hdr, this.line, toStringz(tag), &integer, 1);
        }
        
        else static if(isFloatingPoint!T) {
            auto flt = cast(float) data;    // simply passing "2.0" (or whatever) => data is a double
            ret = bcf_update_format_float(this.vcfheader.hdr, this.line, toStringz(tag), &flt, 1);
        }

        else static if(isSomeString!T)
            ret = bcf_update_format_string(this.vcfheader.hdr, this.line, toStringz(tag), toStringz(data));
        
        else static if(isBoolean!T) {
            immutable int set = data ? 1 : 0; // if data == true, pass 1 to bcf_update_info_flag(n=); n=0 => clear flag 
            ret = bcf_update_format_flag(this.vcfheader.hdr, this.line, toStringz(tag), null, set);
        }
        
        if (ret == -1) hts_log_warning(__FUNCTION__, format("Couldn't add format (ignoring): %s", data));
    }
    /// auto bcf_update_format_int32(const(bcf_hdr_t) *hdr, bcf1_t *line, const(char) *key, int *values, int n) // @suppress(dscanner.style.undocumented_declaration)
    void addFormat(T)(string tag, T[] data)
    {
                int ret = -1;

        static if(isIntegral!T) {
            auto integer = cast(int[]) data;
            ret = bcf_update_format_int32(this.vcfheader.hdr, this.line, toStringz(tag),
                                            integer.ptr, cast(int)data.length);
        }
        
        else static if(isFloatingPoint!T) {
            auto flt = cast(float[]) data;    // simply passing "2.0" (or whatever) => data is a double
            ret = bcf_update_format_float(this.vcfheader.hdr, this.line, toStringz(tag),
                                            flt.ptr, cast(int)data.length);
        }
        
        if (ret == -1) hts_log_warning(__FUNCTION__, format("Couldn't add format (ignoring): %s", data));

    }

    /// add INFO or FORMAT key:value pairs to a record
    /// add a single datapoint OR vector of values, OR, values to each sample (if tagType == FORMAT)
    void add(string tagType, T)(const(char)[] tag, T data)
    if((tagType == "INFO" || tagType == "FORMAT") &&
        (isIntegral!T       || isIntegral!(ElementType!T)   ||
        isFloatingPoint!T   || isFloatingPoint!(ElementType!T) ||
        isSomeString!T      || isSomeString!(ElementType!T) ||
        isBoolean!T         || isBoolean!(ElementType!T)))
    {
        int ret = -1;
        int len;

        static if (!isDynamicArray!T) {
            len = 1;
            static if (isIntegral!T) auto d = data.to!int;
            else static if (isFloatingPoint!T) auto d = data.to!float;
            else static if (isSomeString!T) auto d = toStringz(data);
            else static if (isBoolean!T) immutable int d = data ? 1 : 0; // if data == true, pass 1 to bcf_update_info_flag(n=); n=0 => clear flag
            else static assert(0);

            const auto ptr = &d;
        }
        else static if (isDynamicArray!T) {
            assert(data.length < int.max);
            len = cast(int) data.length;
            static if (isIntegral!(ElementType!T)) auto d = data.to!(int[]);
            else static if (isFloatingPoint!(ElementType!T)) auto d = data.to!(float[]);
            else static if (isSomeString!(ElementType!T)) {
                char[] d;
                foreach(s; data) {
                    d ~= s ~ "\0";
                }
                if(d.length == 0) d ~= "\0";    // TODO replace with asserts on data length earlier
            }
            else static if (isBoolean!(ElementType!T)) {
                int[] d;
                foreach(b; data) {
                    d ~= (b ? 1 : 0);
                }
            }

            const auto ptr = d.ptr;
        }
        else static assert(0);

        static if (tagType == "INFO") {
            static if (is(Unqual!T == int) || is(Unqual!(ElementType!T) == int))
                ret = bcf_update_info_int32(this.vcfheader.hdr, this.line, toStringz(tag), ptr, len);
            else static if (is(Unqual!T == float) || is(Unqual!(ElementType!T) == float))
                ret = bcf_update_info_float(this.vcfheader.hdr, this.line, toStringz(tag), ptr, len);
            else static if (isSomeString!T || isSomeString!(ElementType!T))
                ret = bcf_update_info_string(this.vcfheader.hdr, this.line, toStringz(tag), ptr);
            else static if (is(T == bool) || is(ElementType!T == bool))
                ret = bcf_update_info_flag(this.vcfheader.hdr, this.line, toStringz(tag), ptr, len);
            else static assert(0, "Type not recognized for INFO tag");
        }
        else static if (tagType == "FORMAT") {
            static if (is(Unqual!T == int) || is(Unqual!(ElementType!T) == int))
                ret = bcf_update_format_int32(this.vcfheader.hdr, this.line, toStringz(tag), ptr, len);
            else static if (is(Unqual!T == float) || is(Unqual!(ElementType!T) == float))
                ret = bcf_update_format_float(this.vcfheader.hdr, this.line, toStringz(tag), ptr, len);
            else static if (isSomeString!T || isSomeString!(ElementType!T))
                ret = bcf_update_format_string(this.vcfheader.hdr, this.line, toStringz(tag), ptr, len);
            else static assert(0, "Type not recognized for FORMAT tag");
        }
        else static assert(0);

        if (ret == -1)
            hts_log_warning(__FUNCTION__, format("Couldn't add tag (ignoring): %s with value %s", tag, data));
    }

    override string toString() const
    {
        kstring_t s;

        const int ret = vcf_format(this.vcfheader.hdr, this.line, &s);
        if (ret)
        {
            hts_log_error(__FUNCTION__,
                format("vcf_format returned nonzero (%d) (likely EINVAL, invalid bcf1_t struct?)", ret));
            return "[VCFRecord vcf_format parse_error]";
        }

        return cast(string) s.s[0 .. s.l];
    }
}

/** Basic support for writing VCF, BCF files */
struct VCFWriter
{
    // htslib data structures
    vcfFile     *fp;    /// htsFile
    //bcf_hdr_t   *hdr;   /// header
    VCFHeader   *vcfhdr;    /// header wrapper -- no copies
    bcf1_t*[]    rows;   /// individual records

    @disable this();
    /// open file or network resources for writing
    /// setup incl header allocation
    /// if mode==w:
    ///     bcf_hdr_init automatically sets version string (##fileformat=VCFv4.2)
    ///     bcf_hdr_init automatically adds the PASS filter
    this(string fn)
    {
        if (fn == "") throw new Exception("Empty filename passed to VCFWriter constructor");
        this.fp = vcf_open(toStringz(fn), toStringz("w"c));
        if (!this.fp) throw new Exception("Could not hts_open file");

        this.vcfhdr = new VCFHeader( bcf_hdr_init("w\0"c.ptr));
        addFiledate();
        bcf_hdr_sync(this.vcfhdr.hdr);

        /+
        hts_log_trace(__FUNCTION__, "Displaying header at construction");
        //     int bcf_hdr_format(const(bcf_hdr_t) *hdr, int is_bcf, kstring_t *str);
        kstring_t ks;
        bcf_hdr_format(this.vcfhdr.hdr, 0, &ks);
        char[] hdr;
        hdr.length = ks.l;
        import core.stdc.string: memcpy;
        memcpy(hdr.ptr, ks.s, ks.l);
        import std.stdio: writeln;
        writeln(hdr);
        +/
    }
    /// setup and copy a header from another BCF/VCF as template
    this(T)(string fn, T other)
    if(is(T == VCFHeader*) || is(T == bcf_hdr_t*))
    {
        if (fn == "") throw new Exception("Empty filename passed to VCFWriter constructor");
        this.fp = vcf_open(toStringz(fn), toStringz("w"c));
        if (!this.fp) throw new Exception("Could not hts_open file");

        static if(is(T == VCFHeader*)) { this.vcfhdr      = new VCFHeader( bcf_hdr_dup(other.hdr) ); }
        else static if(is(T == bcf_hdr_t*)) { this.vcfhdr = new VCFHeader( bcf_hdr_dup(other) ); }
    }
    /// dtor
    ~this()
    {
        const ret = vcf_close(this.fp);
        if (ret != 0) hts_log_error(__FUNCTION__, "couldn't close VCF after writing");

        // Deallocate header
        //bcf_hdr_destroy(this.hdr);
        // 2018-09-15: Do not deallocate header; will be free'd by VCFHeader dtor
    }
    invariant
    {
        assert(this.vcfhdr != null);
    }

    VCFHeader* getHeader()
    {
        return this.vcfhdr;
    }

    // TODO
    /// copy header lines from a template without overwiting existing lines
    void copyHeaderLines(bcf_hdr_t *other)
    {
        assert(this.vcfhdr != null);
        assert(0);
        //    bcf_hdr_t *bcf_hdr_merge(bcf_hdr_t *dst, const(bcf_hdr_t) *src);
    }

    /// Add sample to this VCF
    /// * int bcf_hdr_add_sample(bcf_hdr_t *hdr, const(char) *sample);
    int addSample(string name)
    in { assert(name != ""); }
    do
    {
        assert(this.vcfhdr != null);

        bcf_hdr_add_sample(this.vcfhdr.hdr, toStringz(name));

        // AARRRRGGGHHHH
        // https://github.com/samtools/htslib/issues/767
        bcf_hdr_sync(this.vcfhdr.hdr);

        return 0;
    }

    /// Add a new header line
    int addHeaderLineKV(string key, string value)
    {
        // TODO check that key is not INFO, FILTER, FORMAT (or contig?)
        string line = format("##%s=%s", key, value);

        return bcf_hdr_append(this.vcfhdr.hdr, toStringz(line));
    }
    /// Add a new header line -- must be formatted ##key=value
    int addHeaderLineRaw(string line)
    {
        assert(this.vcfhdr != null);
        //    int bcf_hdr_append(bcf_hdr_t *h, const(char) *line);
        const auto ret = bcf_hdr_append(this.vcfhdr.hdr, toStringz(line));
        bcf_hdr_sync(this.vcfhdr.hdr);
        return ret;
    }
    /// Add a filedate= headerline, which is not called out specifically in  the spec,
    /// but appears in the spec's example files. We could consider allowing a param here.
    int addFiledate()
    {
        return addHeaderLineKV("filedate", (cast(Date) Clock.currTime()).toISOString );
    }
    
    /** Add INFO (§1.2.2) or FORMAT (§1.2.4) tag

    The INFO tag describes row-specific keys used in the INFO column;
    The FORMAT tag describes sample-specific keys used in the last, and optional, genotype column.

    Template parameter: string; must be INFO or FORMAT

    The first four parameters are required; NUMBER and TYPE have specific allowable values.
    source and version are optional, but recommended (for INFO only).

    *   id:     ID tag
    *   number: NUMBER tag; here a string because it can also take special values {A,R,G,.} (see §1.2.2)
    *   type:   Integer, Float, Flag, Character, and String
    *   description: Text description; will be double quoted
    *   source:      Annotation source  (eg dbSNP)
    *   version:     Annotation version (eg 142)
    */
    void addTag(string tagType, T)( string id,
                                    T number,
                                    string type,
                                    string description,
                                    string source="",
                                    string _version="")
    if((tagType == "INFO" || tagType == "FORMAT") && (isIntegral!T || isSomeString!T))
    {
        string line;    //  we'll suffix with \0, don't worry

        // check ID
        if (id == "") {
            hts_log_error(__FUNCTION__, "no ID");
            return;
        }

        // check Number is either a special code {A,R,G,.} or an integer
        static if(isSomeString!T) {
        if (number != "A" &&
            number != "R" &&
            number != "G" &&
            number != ".") {
                // not a special ; check if integer
                try {
                    number.to!int;  // don't need to store result, will use format/%s
                }
                catch (ConvException e) {
                    hts_log_error(__FUNCTION__, "Number not A/R/G/. nor an integer");
                    return;
                }
        }
        }

        // check Type
        if (type != "Integer" &&
            type != "Float" &&
            type != "Flag" &&
            type != "Character" &&
            type != "String") {
                hts_log_error(__FUNCTION__, "unrecognized type");
                return;
        }

        // check Description
        if (description == "") hts_log_error(__FUNCTION__, "no description");

        // check Source and Version
        if (source == "" && _version != "") hts_log_error(__FUNCTION__, "version wo source");

        // Format params
        if (source != "" && _version != "")
            line = format("##%s=<ID=%s,Number=%s,Type=%s,Description=\"%s\",Source=\"%s\",Version=\"%s\">\0",
                            tagType, id, number, type, description, source, _version);
        else if (source != "" && _version == "")
            line = format("##%s=<ID=%s,Number=%s,Type=%s,Description=\"%s\",Source=\"%s\">\0",
                            tagType, id, number, type, description, source);
        else
            line = format("##%s=<ID=%s,Number=%s,Type=%s,Description=\"%s\">\0",
                            tagType, id, number, type, description);

        bcf_hdr_append(this.vcfhdr.hdr, line.ptr);
    }

    /** Add FILTER tag (§1.2.3) */
    void addTag(string tagType)(string id, string description)
    if(tagType == "FILTER")
    {
        // check ID
        if (id == "") {
            hts_log_error(__FUNCTION__, "no ID");
            return;
        }
        // check Description
        if (description == "") hts_log_error(__FUNCTION__, "no description");

        string line = format("##FILTER=<ID=%s,Description=\"%s\">\0", id, description);
        bcf_hdr_append(this.vcfhdr.hdr, line.ptr);
    }

    /** Add FILTER tag (§1.2.3) */
    deprecated void addFilterTag(string id, string description)
    {
        string filter = format("##FILTER=<ID=%s,Description=\"%s\">\0", id, description);
        bcf_hdr_append(this.vcfhdr.hdr, filter.ptr);
    }

    /** Add contig definition (§1.2.7) to header meta-info 
    
        other: "url=...,md5=...,etc."
    */
    auto addTag(string tagType)(const(char)[] id, const int length = 0, string other = "")
    if(tagType == "contig" || tagType == "CONTIG")
    {
        const(char)[] contig = "##contig=<ID=" ~ id ~
            (length > 0  ? ",length=" ~ length.to!string : "") ~
            (other != "" ? "," ~ other : "") ~
            ">\0";
        
        return bcf_hdr_append(this.vcfhdr.hdr, contig.ptr);
    }
    
    /**
        Add a record

        alleles:    comma-separated string, including ref allele
        qual:       a float, but accepts any numeric
    */
    int addRecord(S, N)(S contig, int pos, S id, S alleles, N qual, S[] filters)
    if ( (isSomeString!S || is(S == char*) ) && isNumeric!N)
    {        
        bcf1_t *line = new bcf1_t;

        line.rid = bcf_hdr_name2id(this.vcfhdr.hdr, toStringz(contig));
        if (line.rid == -1) hts_log_error(__FUNCTION__, "contig not found");

        line.pos = pos;

        bcf_update_id(this.vcfhdr.hdr, line, (id == "" ? null : toStringz(id)) );  // TODO: could support >1 id with array as with the filters

        bcf_update_alleles_str(this.vcfhdr.hdr, line, toStringz(alleles));

        line.qual = qual;

        // Update filter(s); if/else blocks for speed
        if(filters.length == 0)
        {
            int pass = bcf_hdr_id2int(this.vcfhdr.hdr, BCF_DT_ID, toStringz("PASS"c));
            bcf_update_filter(this.vcfhdr.hdr, line, &pass, 1);
        }
        else if(filters.length == 1)
        {
            int fid = bcf_hdr_id2int(this.vcfhdr.hdr, BCF_DT_ID, toStringz(filters[0]));
            if(fid == -1) hts_log_error(__FUNCTION__, format("filter not found (ignoring): ", filters[0]) );
            bcf_update_filter(this.vcfhdr.hdr, line, &fid, 1);
        }
        else    // TODO: factor out the check for -1 into a safe_update_filter or something
        {
            int[] filter_ids;
            foreach(f; filters) {
                const int fid = bcf_hdr_id2int(this.vcfhdr.hdr, BCF_DT_ID, toStringz(f));
                if(fid == -1) hts_log_error(__FUNCTION__, format("filter not found (ignoring): ", f) );
                else filter_ids ~= fid;
            }
            bcf_update_filter(this.vcfhdr.hdr, line, filter_ids.ptr, cast(int)filter_ids.length );
        }

        // Add a record
        /+
        // .. FORMAT
        bcf_hdr_append(hdr, "##FORMAT=<ID=TF,Number=1,Type=Float,Description=\"Test Float\">");
        float[4] test;
        bcf_float_set_missing(test[0]);
        test[1] = 47.11f;
        bcf_float_set_vector_end(test[2]);
        writeln("pre update format float");
        bcf_update_format_float(this.vcfhdr.hdr, line, toStringz("TF"), &test[0], 4);
        +/
        int tmpi = 1;
        bcf_update_info_int32(this.vcfhdr.hdr, line, toStringz("NS"c), &tmpi, 1);

        // Add the actual sample
        int[4] dp = [ 9000, 1, 2, 3];
        bcf_update_format(this.vcfhdr.hdr, line, toStringz("DP"c), &dp, 1, BCF_HT_INT);
        //int dp = 9000;
        //bcf_update_format_int32(this.vcfhdr.hdr, line, toStringz("DP"c), &dp, 1);
        //auto f = new float;
        //*f = 1.0;
        //bcf_update_format_float(this.vcfhdr.hdr, line, toStringz("XF"c), f, 1);

        this.rows ~= line;

        return 0;
    }

    /// as expected
    int writeHeader()
    {
        return bcf_hdr_write(this.fp, this.vcfhdr.hdr);
    }
    /// as expected
    int writeRecord(ref VCFRecord r)
    {
        const ret = bcf_write(this.fp, this.vcfhdr.hdr, r.line);
        if (ret != 0) hts_log_error(__FUNCTION__, "bcf_write error");
        return ret;
    }
    /// as expected
    int writeRecord(bcf_hdr_t *hdr, bcf1_t *rec)
    {
        hts_log_warning(__FUNCTION__, "pre call");
        const ret = bcf_write(this.fp, hdr, rec);
        hts_log_warning(__FUNCTION__, "post call");
        if (ret != 0) hts_log_error(__FUNCTION__, "bcf_write error");
        return ret;
    }
}

/** Basic support for reading VCF, BCF files */
struct VCFReader
{
    // htslib data structures
    vcfFile     *fp;    /// htsFile
    //bcf_hdr_t   *hdr;   /// header
    VCFHeader   *vcfhdr;    /// header wrapper -- no copies
    bcf1_t* b;          /// record for use in iterator, will be recycled

    int MAX_UNPACK;     /// see dhtslib.htslib.vcf

    private static int refct;

    this(this)
    {
        this.refct++;
    }
    @disable this();
    /// read existing VCF file
    /// MAX_UNPACK: setting alternate value could speed reading
    this(string fn, int MAX_UNPACK = BCF_UN_ALL)
    {
        import dhtslib.htslib.hts : hts_set_threads;

        if (fn == "") throw new Exception("Empty filename passed to VCFReader constructor");
        this.fp = vcf_open(toStringz(fn), "r"c.ptr);
        if (!this.fp) throw new Exception("Could not hts_open file");
        
        hts_set_threads(this.fp, 1);    // extra decoding thread

        this.vcfhdr = new VCFHeader( bcf_hdr_read(this.fp));

        this.b = bcf_init1();
        this.b.max_unpack = MAX_UNPACK;
        this.MAX_UNPACK = MAX_UNPACK;
    }
    /// dtor
    ~this()
    {
        this.refct--;

        // block file close and bcf1_t free() with reference counting
        // to allow VCFReader to implement Range interface
        if(!this.refct) {
            const ret = vcf_close(this.fp);
            if (ret != 0) hts_log_error(__FUNCTION__, "couldn't close VCF after reading");

            // Deallocate header
            //bcf_hdr_destroy(this.hdr);
            // 2018-09-15: Do not deallocate header; will be free'd by VCFHeader dtor

            bcf_destroy1(this.b);
        }
    }
    invariant
    {
        assert(this.vcfhdr != null);
    }

    VCFHeader* getHeader()
    {
        return this.vcfhdr;
    }
    
    /** VCF version, e.g. VCFv4.2 */
    @property string vcfVersion() { return cast(string) fromStringz( bcf_hdr_get_version(this.vcfhdr.hdr) ).idup; }

    /++
        bcf_hrec_t *bcf_hdr_get_hrec(const(bcf_hdr_t) *hdr, int type, const(char) *key, const(char) *value,
                                                                                    const(char) *str_class);
    +/
    // TODO: check key for "", fail if empty
    // TODO: check value, str_class for "" and replace with NULL
    // TODO: Memory leak. We are never freeing the bcf_hrec_t, but, it escapes as pointer inside key/value string
    // TODO: handle structured and general lines
    string[string] getTagByKV(string tagType, T)(string key, string value, string str_class)
    if((tagType == "FILTER" || tagType == "INFO" || tagType == "FORMAT" && tagType == "contig") &&
        (isIntegral!T || isSomeString!T))
    {
        // hlt : header line type
        static if (tagType == "FILTER")     const int hlt = BCF_HL_FLT;
        else static if (tagType == "INFO")  const int hlt = BCF_HL_INFO; // @suppress(dscanner.suspicious.label_var_same_name)
        else static if (tagType == "FORMAT") const int hlt= BCF_HL_FMT; // @suppress(dscanner.suspicious.label_var_same_name)
        else static if (tagType == "contig") const int hlt= BCF_HL_CTG; // @suppress(dscanner.suspicious.label_var_same_name)
        else assert(0);

        bcf_hrec_t *hrec = bcf_hdr_get_hrec(this.vcfhdr.hdr, hlt,   toStringz(key),
                                                                    toStringz(value),
                                                                    toStringz(str_class));

        const int nkeys = hrec.nkeys;
        string[string] kv;

        foreach(int i; 0 .. nkeys) {
            string k = cast(string) fromStringz(hrec.keys[i]);
            string v = cast(string) fromStringz(hrec.vals[i]); 
            kv[k] = v;
        }

        return kv;
    }

    /// InputRange interface: iterate over all records
    @property bool empty()
    {
        //     int bcf_read(htsFile *fp, const(bcf_hdr_t) *h, bcf1_t *v);
        // documentation claims returns -1 on critical errors, 0 otherwise
        // however it looks like -1 is EOF and -2 is critical errors?
        immutable success = bcf_read(this.fp, this.vcfhdr.hdr, this.b);
        if (success >= 0) return false;
        else if (success == -1) {
            // EOF
            // see htslib my comments https://github.com/samtools/htslib/issues/246
            // and commit 9845bc9a947350d0f34e6ce69e79ab81b6339bd2
            return true;
        }
        else {
            hts_log_error(__FUNCTION__, "*** CRITICAL ERROR bcf_read < -1");
            // TODO: check b->errcode
            return true;
        }
    }
    /// ditto
    void popFront()
    {
        // noop? 
        // free this.b ?
        //bam_destroy1(this.b);

        // TODO: clear (not destroy) the bcf1_t for reuse?
    }
    /// ditto
    VCFRecord front()
    {
        // note that VCFRecord's constructor will be responsible for
        // * unpacking and
        // * destroying
        // its copy
        return new VCFRecord(this.vcfhdr, bcf_dup(this.b), this.MAX_UNPACK);
    }
}

///
debug(dhtslib_unittest)
unittest
{
    import std.exception: assertThrown;
    import std.stdio: writeln, writefln;

    hts_set_log_level(htsLogLevel.HTS_LOG_TRACE);


    auto vw = VCFWriter("/dev/null");

    vw.addHeaderLineRaw("##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">");
    vw.addHeaderLineKV("INFO", "<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">");
    // ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
    vw.addTag!"INFO"("AF", "A", "Integer", "Number of Samples With Data");
    vw.addHeaderLineRaw("##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species=\"Homo sapiens\",taxonomy=x>"); // @suppress(dscanner.style.long_line)
    vw.addHeaderLineRaw("##FILTER=<ID=q10,Description=\"Quality below 10\">");

    // Exercise header
    assert(vw.vcfhdr.nsamples == 0);
    vw.addSample("NA12878");
    assert(vw.vcfhdr.nsamples == 1);

    auto r = new VCFRecord(vw.vcfhdr, bcf_init1());
    
    r.chrom = "20";
    assert(r.chrom == "20");
    assertThrown(r.chrom = "chr20");   // headerline chromosome is "20" not "chr20"

    r.pos = 999_999;
    assert(r.pos == 999_999);
    r.pos = 62_435_964 + 1;     // Exceeds contig length

    // Test ID field
    // note that in an empty freshly initialized bcf1_t, the ID field is "" rather than "."
    // Will consider adding initialization code
    //writefln("ID: %s", r.id);
    r.id = "";
    assert(r.id == ".");
    r.id = ".";
    assert(r.id == ".");
    r.id = "rs001";
    assert(r.id == "rs001");
    r.addID("rs999");
    assert(r.id == "rs001;rs999");
    r.addID("rs001");   // test duplicate checking
    assert(r.id == "rs001;rs999");

    // Test REF/ALT allele setters and getters
    // many overloads to test for good coverage
    // Test matrix: Set {zero, one, two, three} alleles * {set by string, set by array} = 8 test cases
    //  * also, there is setAlleles(ref, alt) and setAlleles(ref, alt1, ...) 
    //  * TODO: will also need to retreive alt alleles as array and string

    string[] alleles_array;

    // Zero alleles
    r.alleles("");
    const auto zs = r.allelesAsArray;
    const auto zsr = r.refAllele;
    assert(zs.length == 0);
    assert(zsr == "");

    r.alleles(alleles_array);
    const auto za = r.allelesAsArray;
    const auto zar = r.refAllele;
    assert(za.length == 0);
    assert(zar == "");
    
    // One allele
    r.alleles("C");
    const auto os = r.allelesAsArray;
    const auto osr = r.refAllele;
    assert(os.length == 1 && os[0] == "C");
    assert(osr == "C");

    r.alleles(["C"]);
    const auto oa = r.allelesAsArray;
    const auto oar = r.refAllele;
    assert(oa.length == 1 && oa[0] == "C");
    assert(oar == "C");

    // Two alleles
    r.alleles("C,T");
    const auto ts = r.allelesAsArray;
    const auto tsr= r.refAllele;
    assert(ts == ["C", "T"]);
    assert(tsr== "C");

    r.alleles(["C", "T"]);
    const auto ta = r.allelesAsArray;
    const auto tar= r.refAllele;
    assert(ta == ["C", "T"]);
    assert(tar== "C");

    const taaa = r.altAllelesAsArray;
    const taas = r.altAllelesAsString;
    assert(taaa == ["T"]);
    assert(taas == "T");

    // alternate setter for >= 2 alleles
    r.setAlleles("A", "G");
    assert(r.allelesAsArray == ["A", "G"]);

    // Three alleles
    r.alleles("A,C,T");
    assert(r.allelesAsArray == ["A", "C", "T"]);
    assert(r.refAllele == "A");
    assert(r.altAllelesAsString == "C,T");

    // alternate the alleles for testing purposes
    r.alleles(["G", "A", "C"]);
    assert(r.allelesAsArray == ["G", "A", "C"]);
    assert(r.refAllele == "G");
    assert(r.altAllelesAsString == "A,C");

    r.setAlleles("A", "C", "T");
    assert(r.allelesAsArray == ["A", "C", "T"]);
    assert(r.refAllele == "A");
    assert(r.altAllelesAsString == "C,T");


    // Test QUAL
    r.qual = 1.0;
    assert(r.qual == 1.0);
    // now test setting qual without unpacking
    // TODO: see https://forum.dlang.org/post/hebouvswxlslqhovzaia@forum.dlang.org, once resolved (or once factory function written),
    //  add template value param BCF_UN_STR
    auto rr = new VCFRecord(vw.vcfhdr, "20\t17330\t.\tT\tA\t3\t.\tNS=3;DP=11;AF=0.017\n"); // @suppress(dscanner.style.long_line)
    rr.qual = 3.0;
    assert(rr.qual == 3.0);


    // Test FILTER
    assert(r.hasFilter("PASS"));
    assert(r.hasFilter("."));
    // add q10 filter (is in header)
    r.filter = "q10";
    assert(r.filter == "q10");
    assert(!r.hasFilter("PASS"));   // if has another filter, no longer PASS (unless added explicitly)
    assert(!r.hasFilter("."));      // if has another filter, no longer has . (which is PASS, or no filter [spec conflict?])

    // add q30 filteR (not in header)
    r.filter = "q30";
    assert(r.filter == "q10");  // i.e., unchanged

    assert(r.hasFilter("q10"));
    assert(!r.hasFilter("q30"));

    r.removeAllFilters();
    assert(r.hasFilter("."));
    r.addFilter("q10");
    assert(r.hasFilter("q10"));
    r.removeFilter("q10");
    assert(r.hasFilter("PASS"));


    // Finally, print the records:
    writefln("VCF records via toString:\n%s%s", r, rr);

    writeln("\ndhtslib.vcf: all tests passed\n");
}