r246: all translation tables

Thanks to @giacomomutti in #57

main.c

@@ -55,7 +55,7 @@ static void print_usage(FILE *fp, const mp_idxopt_t *io, const mp_mapopt_t *mo,
 	fprintf(fp, "    -k INT       k-mer size [%d]\n", io->kmer);
 	fprintf(fp, "    -M INT       modimisers bit (sample rate = 1/2**M) [%d]\n", io->mod_bit);
 	fprintf(fp, "    -L INT       min ORF length to index [%d]\n", io->min_aa_len);
-	fprintf(fp, "    -T INT       NCBI translation table (from 1 to 5) [%d]\n", io->trans_code);
+	fprintf(fp, "    -T INT       NCBI translation table (1 through 33) [%d]\n", io->trans_code);
 	fprintf(fp, "    -b INT       bits per block [%d]\n", io->bbit);
 	fprintf(fp, "    -d FILE      save index to FILE []\n");
 	fprintf(fp, "  Mapping:\n");

miniprot.1

@@ -48,7 +48,7 @@ Sample k-mers at a rate
 Minimum ORF length to index [30]
 .TP
 .BI -T \ INT
-NCBI translation table (1 through 5) [1]
+NCBI translation table (1 through 33 except 7-8 and 17-20) [1]
 .TP
 .BI -b \ INT
 Number of bits per bin [8]. Miniprot splits the genome into non-overlapping bins of 2^8 bp in size.

miniprot.h

@@ -3,7 +3,7 @@
 
 #include <stdint.h>
 
-#define MP_VERSION "0.12-r245-dirty"
+#define MP_VERSION "0.12-r246-dirty"
 
 #define MP_F_NO_SPLICE    0x1
 #define MP_F_NO_ALIGN     0x2

nasw-tab.c

@@ -12,7 +12,7 @@ char *ns_tab_aa_i2c = "ARNDCQEGHILKMFPSTWYV*X";
 uint8_t ns_tab_a2r[22] = { 0, 2, 4, 4, 6, 5, 5, 8, 3, 10, 11, 2, 11, 12, 7, 1, 1, 13, 12, 10, 14, 15 };
 						// A  R  N  D  C  Q  E  G  H   I   L  K   M   F  P  S  T   W   Y   V   *   X
 
-#define NS_MAX_TRANS_CODE 5
+#define NS_MAX_TRANS_CODE 33
 static const char *ns_tab_codon_all[NS_MAX_TRANS_CODE + 1] = {
    0,
  // 0123456789012345678901234567890123456789012345678901234567890123
@@ -24,6 +24,34 @@ static const char *ns_tab_codon_all[NS_MAX_TRANS_CODE + 1] = {
    "KNKNTTTTRSRSMIMIQHQHPPPPRRRRTTTTEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLFX", // 3: The Yeast Mitochondrial Code
    "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLFX", // 4: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
    "KNKNTTTTSSSSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLFX"  // 5: The Invertebrate Mitochondrial Code
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVQYQYSSSS*CWCLFLFX", // 6: Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
+   0, // 7
+   0, // 8
+   "NNKNTTTTSSSSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLFX", // 9: Echinoderm Mitochondrial; Flatworm Mitochondrial
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSCCWCLFLFX", // 10: Euplotid Nuclear
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLFX", // 11: Bacterial, Archaeal and Plant Plastid
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLSLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLFX", // 12: Alternative Yeast Nuclear
+   "KNKNTTTTGSGSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLFX", // 13: Ascidian Mitochondrial
+   "NNKNTTTTSSSSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVYY*YSSSSWCWCLFLFX", // 14: Alternative Flatworm Mitochondrial
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YQYSSSS*CWCLFLFX", // 15: Blepharisma Macronuclear
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YLYSSSS*CWCLFLFX", // 16: Chlorophycean Mitochondrial
+   0, // 17
+   0, // 18
+   0, // 19
+   0, // 20
+   "NNKNTTTTSSSSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLFX", // 21: Trematode Mitochondrial
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YLY*SSS*CWCLFLFX", // 22: Scenedesmus obliquus Mitochondrial
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWC*FLFX", // 23: Thraustochytrium Mitochondrial
+   "KNKNTTTTSSKSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLFX", // 24: Rhabdopleuridae Mitochondrial
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSGCWCLFLFX", // 25: Candidate Division SR1 and Gracilibacteria
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLALEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLFX", // 26: Pachysolen tannophilus Nuclear
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVQYQYSSSSWCWCLFLFX", // 27: Karyorelict Nuclear
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVQYQYSSSSWCWCLFLFX", // 28: Condylostoma Nuclear
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVYYYYSSSS*CWCLFLFX", // 29: Mesodinium Nuclear
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVEYEYSSSS*CWCLFLFX", // 30: Peritrich Nuclear
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVEYEYSSSSWCWCLFLFX", // 31: Blastocrithidia Nuclear
+   "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YWYSSSS*CWCLFLFX", // 32: Balanophoraceae Plastid
+   "KNKNTTTTSSKSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVYY*YSSSSWCWCLFLFX", // 33: Cephalodiscidae Mitochondrial
 };
 
 uint8_t ns_tab_nt4[256], ns_tab_aa20[256], ns_tab_aa13[256], ns_tab_codon[64], ns_tab_codon13[64];