add --strict mode

doc/quaqc.1

@@ -292,6 +292,12 @@ Set \f[C]--use-nomate\f[R], \f[C]--use-dups\f[R],
 This relaxes the filtering parameters, allowing a greater number of
 reads to be counted for QC.
 .TP
+\f[B]--strict\f[R]
+Set \f[C]--min-flen=50\f[R], \f[C]--max-flen=150\f[R], and
+\f[C]--mapq=40\f[R].
+This restricts the filtering parameters to keep only the highest quality
+reads.
+.TP
 \f[B]--nfr\f[R]
 Set \f[C]--no-se\f[R], \f[C]--max-flen=120\f[R], and
 \f[C]--tss-tn5\f[R].

doc/quaqc.1.md

@@ -248,6 +248,11 @@ accomplished using `samtools` in the following manner during alignment:
     relaxes the filtering parameters, allowing a greater number of reads to be
     counted for QC.
 
+**\--strict**
+:   Set `--min-flen=50`, `--max-flen=150`, and `--mapq=40`. This
+    restricts the filtering parameters to keep only the highest quality
+    reads.
+
 **\--nfr**
 :   Set `--no-se`, `--max-flen=120`, and `--tss-tn5`. These filters enrich for
     reads found within nucleosome free regions (NFR), as well as shifting the

src/output.c

@@ -233,6 +233,7 @@ int init_json(const params_t *params) {
   fjson_write(fjson, "    \"fast_mode\": %s,\n", strbool(params->fast));
   fjson_write(fjson, "    \"low_mem_mode\": %s,\n", strbool(params->low_mem));
   fjson_write(fjson, "    \"lenient_mode\": %s,\n", strbool(params->lenient));
+  fjson_write(fjson, "    \"strict_mode\": %s,\n", strbool(params->strict));
   fjson_write(fjson, "    \"nfr_mode\": %s,\n", strbool(params->nfr));
   fjson_write(fjson, "    \"nbr_mode\": %s,\n", strbool(params->nbr));
   fjson_write(fjson, "    \"footprint_mode\": %s,\n", strbool(params->footprint));

src/quaqc.c

@@ -116,6 +116,7 @@ enum opts_enum {
   TSS_QLEN,
   TN5_SHIFT,
   LENIENT,
+  STRICT,
   NFR,
   NBR,
   NO_SE,
@@ -152,6 +153,7 @@ static struct option opts_long[] = {
   { "tss-tn5",       no_argument,       0, TN5_SHIFT     },
   { "use-all",       no_argument,       0, USE_ALL       },
   { "lenient",       no_argument,       0, LENIENT       },
+  { "strict",        no_argument,       0, STRICT        },
   { "nfr",           no_argument,       0, NFR           },
   { "nbr",           no_argument,       0, NBR           },
   { "footprint",     no_argument,       0, FOOTPRINT     },
@@ -229,6 +231,7 @@ static void help(void) {
     " -f, --fast                 --omit-gc --omit-depth (~15%% shorter runtime)\n"
     /* " -L, --low-mem              --max-depth=1 --max-qhist=1 --max-fhist=1 --tss-size=1\n" */ // hide for now
     "     --lenient              --use-nomate --use-dups --use-dovetails --mapq=10\n"
+    "     --strict               --min-flen=50 --max-flen=150 --mapq=40\n"
     "     --nfr                  --no-se --max-flen=120 --tss-tn5\n"
     "     --nbr                  --no-se --min-flen=150 --max-flen=1000 --tss-qlen=0\n"
     "     --footprint            --tss-qlen=1 --tss-size=501 --tss-tn5\n"
@@ -889,6 +892,12 @@ static int quaqc_main(int argc, char *argv[]) {
         }
         params->lenient = true;
         break;
+      case STRICT:
+        if (params->strict) {
+          quit("--strict has already been set.");
+        }
+        params->strict = true;
+        break;
       case NFR:
         if (params->nfr) {
           quit("--nfr has already been set.");
@@ -1067,6 +1076,12 @@ static int quaqc_main(int argc, char *argv[]) {
     params->use_dovetail = true;
   }
 
+  if (params->strict) {
+    params->flen_min = 50;
+    params->flen_max = 150;
+    params->mapq = 40;
+  }
+
   if (params->nbr && params->nfr) {
     quit("--nfr and --nbr cannot be set simultaneously.");
   }

src/quaqc.h

@@ -104,7 +104,7 @@ typedef struct params_t {
   hts_pos_t qlen_min, flen_min, qlen_max, flen_max;
   int threads, depth_max, qhist_max, fhist_max, tss_size, tss_qlen;
   bool use_2nd, use_chi, use_nomate, use_dups, use_all;
-  bool lenient, nfr, nbr, use_dovetail;
+  bool lenient, strict, nfr, nbr, use_dovetail;
   bool no_se, no_out, save, tn5_shift, omit_gc, omit_depth;
   bool fast, qerr, v, vv, footprint, low_mem, chip;
 } params_t;