moving functions from VCFWriter to VCFHeader as appropriate as well a…

…s some unittests, starting work on #96, #94, #69

source/dhtslib/vcf/header.d

@@ -1,8 +1,13 @@
 module dhtslib.vcf.header;
 
+import std.datetime;
 import std.string: fromStringz, toStringz;
+import std.format: format;
+import std.traits : isArray, isIntegral, isSomeString;
+import std.conv: to, ConvException;
 
 import htslib.vcf;
+import htslib.hts_log;
 
 /** Wrapper around bcf_hdr_t
 
@@ -35,6 +40,11 @@ struct VCFHeader
         assert(this.hdr != null);
     }
 
+    /// copy this header
+    auto dup(){
+        return VCFHeader(bcf_hdr_dup(this.hdr));
+    }
+
     /// List of contigs in the header
     @property string[] sequences()
     {
@@ -61,4 +71,196 @@ struct VCFHeader
     pragma(inline, true)
     @property int nsamples() { return bcf_hdr_nsamples(this.hdr); }
 
+    // TODO
+    /// copy header lines from a template without overwiting existing lines
+    void copyHeaderLines(bcf_hdr_t *other)
+    {
+        assert(this.hdr != 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.hdr != null);
+
+        bcf_hdr_add_sample(this.hdr, toStringz(name));
+
+        // AARRRRGGGHHHH
+        // https://github.com/samtools/htslib/issues/767
+        bcf_hdr_sync(this.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.hdr, toStringz(line));
+    }
+    /// Add a new header line -- must be formatted ##key=value
+    int addHeaderLineRaw(string line)
+    {
+        assert(this.hdr != null);
+        //    int bcf_hdr_append(bcf_hdr_t *h, const(char) *line);
+        const auto ret = bcf_hdr_append(this.hdr, toStringz(line));
+        bcf_hdr_sync(this.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.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.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.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.hdr, contig.ptr);
+    }
+}
+
+///
+debug(dhtslib_unittest)
+unittest
+{
+    import std.exception: assertThrown;
+    import std.stdio: writeln, writefln;
+
+    hts_set_log_level(htsLogLevel.HTS_LOG_TRACE);
+
+
+    auto hdr = VCFHeader(bcf_hdr_init("w\0"c.ptr));
+
+    hdr.addHeaderLineRaw("##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">");
+    hdr.addHeaderLineKV("INFO", "<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">");
+    // ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
+    hdr.addTag!"INFO"("AF", "A", "Integer", "Number of Samples With Data");
+    hdr.addHeaderLineRaw("##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species=\"Homo sapiens\",taxonomy=x>"); // @suppress(dscanner.style.long_line)
+    hdr.addHeaderLineRaw("##FILTER=<ID=q10,Description=\"Quality below 10\">");
+
+    // Exercise header
+    assert(hdr.nsamples == 0);
+    hdr.addSample("NA12878");
+    assert(hdr.nsamples == 1);
 }