Added some comments RE #80

CSB5 · Jan 17, 2020 · a4db88e · a4db88e
1 parent ca0bab0
commit a4db88e
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Showing 2 changed files with 12 additions and 4 deletions.
diff --git a/src/lofreq/lofreq_call.c b/src/lofreq/lofreq_call.c
@@ -819,7 +819,7 @@ call_snvs(const plp_col_t *p, varcall_conf_t *conf)
            long double pvalue = pvalues[i];
            int reported_snv_ref = p->ref_base;
 
-           if (alt_base==reported_snv_ref) { 
+           if (alt_base==reported_snv_ref) {
                 /* self comparison */
 #if DEBUG
                 LOG_DEBUG("%s\n", "continue because self comparison")
@@ -830,8 +830,13 @@ call_snvs(const plp_col_t *p, varcall_conf_t *conf)
            if (pvalue * (double)conf->bonf_subst < conf->sig) {
                 const int is_indel = 0;
                 const int is_consvar = 0;
-                float af = alt_raw_count/(float)p->coverage_plp;
-
+		float af = alt_raw_count/(float)p->coverage_plp;
+                /* can we make sure base filtering doesn't affect AF?
+		 * See eg https://github.com/CSB5/lofreq/issues/80
+		 * float af = alt_raw_count/(float)p->num_bases;
+		 * doesn't help either 
+		 */
+                assert(p->num_bases >= alt_raw_count);
                 char report_ref[2];
                 char report_alt[2];
                 report_ref[0] = reported_snv_ref;

diff --git a/src/lofreq/snpcaller.c b/src/lofreq/snpcaller.c
@@ -406,7 +406,10 @@ plp_to_errprobs(double **err_probs, int *num_err_probs,
                if (p->base_quals[i].n) {
                     bq = p->base_quals[i].data[j];
 
-                    /* bq filtering for all */
+                    /* bq filtering for all
+                     * FIXME min_bq was meant to just influence quality calculations, not af etc
+                     * but the filtering leaks out later, because alt_counts is computed and returned after filtering
+                     */
                     if (bq < conf->min_bq) {
                          continue;
                     }