Rename mpileup --edlib to --indels-cns

The main benefit of the new indel caller is the use of alignment
against diploid consensus generation instead of simply patching the
reference with candidate indel types.

This greatly reduces false positives and incorrect allele alignment
(leading to wrong genotype calls).  This was the earlier PR samtools#1679, but
has since acquired edlib as an alternative to BAQ for the indel
alignment.  However this is primarily a speed benefit (with some
minor removal of false-negatives due to quality smashing), and
isn't the main thing users should think about when choosing an indel
caller.

mpileup.c

@@ -1286,27 +1286,27 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
         "      --indel-size INT    Approximate maximum indel size considered [%d]\n", mplp->indel_win_size);
     fprintf(fp,
         "      --indels-2.0        New EXPERIMENTAL indel calling model (diploid reference consensus)\n"
-        "      --edlib             New EXPERIMENTAL indel calling model with edlib\n"
-        "      --no-edlib          Disable edlib mode, to use after a -X profile\n"
+        "      --indels-cns        New EXPERIMENTAL indel calling model with edlib\n"
+        "      --no-indels-cns     Disable CNS mode, to use after a -X profile\n"
         "      --poly-mqual        (Edlib mode) Use minimum quality within homopolymers\n");
     fprintf(fp,"\n");
     fprintf(fp,
         "Configuration profiles activated with -X, --config:\n"
         "    1.12:        -Q13 -h100 -m1 -F0.002\n"
         "    illumina-1.18: --indel-size 110\n"
-        "    illumina or illumina-1.20:    --edlib\n"
+        "    illumina or illumina-1.20:    --indels-cns\n"
         "    ont:         -B -Q5 --max-BQ 30 -I [also try eg |bcftools call -P0.01]\n"
         "    ont-sup or ont-sup-1.20:\n"
         "                     -B -Q1 --max-BQ 99 -F0.20 -o15 -e1  -h80  --delta-BQ 60 \\\n"
-        "                     --del-bias 0.4 --poly-mqual --edlib\n"
+        "                     --del-bias 0.4 --poly-mqual --indels-cns\n"
         "    pacbio-ccs-1.18:  -D -Q5 --max-BQ 50 -F0.1 -o25 -e1 --delta-BQ 10 \\\n"
         "                      -M99999 --indel-size 110\n"
         "    pacbio-ccs or pacbio-ccs-1.20:\n"
         "                 -B -Q5 --max-BQ 50 -F0.10 -o25 -e1  -h300 --delta-BQ 10 \\\n"
-        "                     --del-bias 0.4 --poly-mqual --edlib\n"
+        "                     --del-bias 0.4 --poly-mqual --indels-cns\n"
         "    ultima or ultima-1.20:\n"
-        "                 -B --max-BQ 30 -F0.15 -o20 -e15 -h250 --delta-BQ 10 \\\n"
-        "                     --del-bias 0.3 --poly-mqual --edlib\n"
+        "                 -B --max-BQ 30 -F0.15 -o20 -e10 -h250 --delta-BQ 10 \\\n"
+        "                     --del-bias 0.3 --poly-mqual --indels-cns\n"
         "\n"
         "Notes: Assuming diploid individuals.\n"
         "\n"
@@ -1412,8 +1412,8 @@ int main_mpileup(int argc, char *argv[])
         {"indel-bias", required_argument, NULL, 10},
         {"indel-size", required_argument, NULL, 15},
         {"indels-2.0", no_argument, NULL, 20},
-        {"edlib", no_argument, NULL, 22},
-        {"no-edlib", no_argument, NULL, 25},
+        {"indels-cns", no_argument, NULL, 22},
+        {"no-indels-cns", no_argument, NULL, 25},
         {"tandem-qual", required_argument, NULL, 'h'},
         {"skip-indels", no_argument, NULL, 'I'},
         {"max-idepth", required_argument, NULL, 'L'},