added more info to output stats

najoshi · najoshi · commit 7667f147e6e0 · 2014-07-26T03:15:27.000-07:00
diff --git a/src/trim_paired.c b/src/trim_paired.c
@@ -117,6 +117,7 @@ int paired_main(int argc, char *argv[]) {
     int gzip_output = 0;
     int combo_all=0;
     int combo_s=0;
+    int total=0;
 
     while (1) {
         int option_index = 0;
@@ -375,6 +376,7 @@ int paired_main(int argc, char *argv[]) {
 
         p1cut = sliding_window(fqrec1, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, debug);
         p2cut = sliding_window(fqrec2, qualtype, paired_length_threshold, paired_qual_threshold, no_fiveprime, trunc_n, debug);
+        total += 2;
 
         if (debug) printf("p1cut: %d,%d\n", p1cut->five_prime_cut, p1cut->three_prime_cut);
         if (debug) printf("p2cut: %d,%d\n", p2cut->five_prime_cut, p2cut->three_prime_cut);
@@ -478,6 +480,9 @@ int paired_main(int argc, char *argv[]) {
     }
 
     if (!quiet) {
+        if (infn1 && infn2) fprintf(stdout, "\nPE forwrd file: %s\nPE reverse file: %s\n", infn1, infn2);
+        if (infnc) fprintf(stdout, "\nPE interleaved file: %s\n", infnc);
+        fprintf(stdout, "\nTotal input FastQ records: %d (%d pairs)\n", total, (total / 2));
         fprintf(stdout, "\nFastQ paired records kept: %d (%d pairs)\n", kept_p, (kept_p / 2));
         if (pec) fprintf(stdout, "FastQ single records kept: %d\n", (kept_s1 + kept_s2));
         else fprintf(stdout, "FastQ single records kept: %d (from PE1: %d, from PE2: %d)\n", (kept_s1 + kept_s2), kept_s1, kept_s2);
diff --git a/src/trim_single.c b/src/trim_single.c
@@ -72,6 +72,7 @@ int single_main(int argc, char *argv[]) {
     int no_fiveprime = 0;
     int trunc_n = 0;
     int gzip_output = 0;
+    int total=0;
 
     while (1) {
         int option_index = 0;
@@ -192,6 +193,7 @@ int single_main(int argc, char *argv[]) {
     while ((l = kseq_read(fqrec)) >= 0) {
 
         p1cut = sliding_window(fqrec, qualtype, single_length_threshold, single_qual_threshold, no_fiveprime, trunc_n, debug);
+        total++;
 
         if (debug) printf("P1cut: %d,%d\n", p1cut->five_prime_cut, p1cut->three_prime_cut);
 
@@ -215,7 +217,7 @@ int single_main(int argc, char *argv[]) {
         free(p1cut);
     }
 
-    if (!quiet) fprintf(stdout, "\nFastQ records kept: %d\nFastQ records discarded: %d\n\n", kept, discard);
+    if (!quiet) fprintf(stdout, "\nSE input file: %s\n\nTotal FastQ records: %d\nFastQ records kept: %d\nFastQ records discarded: %d\n\n", infn, total, kept, discard);
 
     kseq_destroy(fqrec);
     gzclose(se);
