diff --git a/src/trim_paired.c b/src/trim_paired.c index d7b58f2..f63b877 100644 --- 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 index b9d9972..44fe013 100644 --- 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);