Add initial support for VCFv4.4 / VCFv4.5 Number= fields

Adds BCF_VL_* types for Number= P, LA, LG, LR and M

Upgrades bcf_hdr_register_hrec() so that it sets the appropriate
value when it finds one of the ne types in a FORMAT header line.

Only set number type BCF_VL_FIXED if the value can actually be
parsed as an integer.  Unknown types will now cause a warning
to be printed and will be treated as BCF_VL_VAR.

Adds doxygen style comments to describe the meaning of the various
BCF_VL_* values.

htslib/vcf.h

@@ -65,11 +65,21 @@ extern "C" {
 #define BCF_HT_STR  3
 #define BCF_HT_LONG (BCF_HT_INT | 0x100) // BCF_HT_INT, but for int64_t values; VCF only!
 
-#define BCF_VL_FIXED 0 // variable length
-#define BCF_VL_VAR   1
-#define BCF_VL_A     2
-#define BCF_VL_G     3
-#define BCF_VL_R     4
+// Values for INFO / FORMAT "Number=" fields
+#define BCF_VL_FIXED 0 ///< Integer defining a fixed number of items
+#define BCF_VL_VAR   1 ///< Generic variable length ("Number=.")
+#define BCF_VL_A     2 ///< One value per alternate allele
+#define BCF_VL_G     3 ///< One value for each possible genotype
+#define BCF_VL_R     4 ///< One value for each allele, including the reference
+
+// The following was introduced in VCFv4.4 and is only valid for FORMAT header lines
+#define BCF_VL_P     5 ///< One value for each allele value defined in GT
+
+// The following were introduced in VCFv4.5 and are only valid for FORMAT header lines
+#define BCF_VL_LA    6 ///< As BCF_VL_A, but only alt alleles listed in LAA are considered present
+#define BCF_VL_LG    7 ///< As BCF_VL_G, but only alt alleles listed in LAA are considered present
+#define BCF_VL_LR    8 ///< As BCF_VL_R, but only alt alleles listed in LAA are considered present
+#define BCF_VL_M     9 ///< One value for each possible base modification for the corresponding ChEBI ID
 
 /* === Dictionary ===
 

vcf.c

@@ -846,14 +846,20 @@ static int bcf_hdr_register_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
         }
         else if ( !strcmp(hrec->keys[i], "Number") )
         {
+            int is_fmt = hrec->type == BCF_HL_FMT;
             if ( !strcmp(hrec->vals[i],"A") ) var = BCF_VL_A;
             else if ( !strcmp(hrec->vals[i],"R") ) var = BCF_VL_R;
             else if ( !strcmp(hrec->vals[i],"G") ) var = BCF_VL_G;
             else if ( !strcmp(hrec->vals[i],".") ) var = BCF_VL_VAR;
+            else if ( is_fmt && !strcmp(hrec->vals[i],"P") )  var = BCF_VL_P;
+            else if ( is_fmt && !strcmp(hrec->vals[i],"LA") ) var = BCF_VL_LA;
+            else if ( is_fmt && !strcmp(hrec->vals[i],"LR") ) var = BCF_VL_LR;
+            else if ( is_fmt && !strcmp(hrec->vals[i],"LG") ) var = BCF_VL_LG;
+            else if ( is_fmt && !strcmp(hrec->vals[i],"M") )  var = BCF_VL_M;
             else
             {
-                sscanf(hrec->vals[i],"%d",&num);
-                var = BCF_VL_FIXED;
+                if (sscanf(hrec->vals[i],"%d",&num) == 1)
+                    var = BCF_VL_FIXED;
             }
             if (var != BCF_VL_FIXED) num = 0xfffff;
         }
@@ -864,7 +870,7 @@ static int bcf_hdr_register_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
                 *hrec->key == 'I' ? "An" : "A", hrec->key);
             type = BCF_HT_STR;
         }
-        if (var == -1) {
+        if (var == UINT32_MAX) {
             hts_log_warning("%s %s field has no Number defined. Assuming '.'",
                 *hrec->key == 'I' ? "An" : "A", hrec->key);
             var = BCF_VL_VAR;