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Use stderr for all logging messages #43

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10 changes: 5 additions & 5 deletions src/sliding.c
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Original file line number Diff line number Diff line change
Expand Up @@ -65,13 +65,13 @@ cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int

window_avg = (double)window_total / (double)window_size;

if (debug) printf ("no_fiveprime: %d, found 5prime: %d, window_avg: %f\n", no_fiveprime, found_five_prime, window_avg);
if (debug) fprintf(stderr, "no_fiveprime: %d, found 5prime: %d, window_avg: %f\n", no_fiveprime, found_five_prime, window_avg);

/* Finding the 5' cutoff */
/* Find when the average quality in the window goes above the threshold starting from the 5' end */
if (no_fiveprime == 0 && found_five_prime == 0 && window_avg >= qual_threshold) {

if (debug) printf ("inside 5-prime cut\n");
if (debug) fprintf(stderr, "inside 5-prime cut\n");

/* at what point in the window does the quality go above the threshold? */
for (j=window_start; j<window_start+window_size; j++) {
Expand All @@ -81,7 +81,7 @@ cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int
}
}

if (debug) printf ("five_prime_cut: %d\n", five_prime_cut);
if (debug) fprintf(stderr, "five_prime_cut: %d\n", five_prime_cut);

found_five_prime = 1;
}
Expand Down Expand Up @@ -125,10 +125,10 @@ cutsites* sliding_window (kseq_t *fqrec, int qualtype, int length_threshold, int
three_prime_cut = -1;
five_prime_cut = -1;

if (debug) printf("%s\n", fqrec->name.s);
if (debug) fprintf(stderr, "%s\n", fqrec->name.s);
}

if (debug) printf ("\n\n");
if (debug) fprintf(stderr, "\n\n");

retvals = (cutsites*) malloc (sizeof(cutsites));
retvals->three_prime_cut = three_prime_cut;
Expand Down
22 changes: 11 additions & 11 deletions src/trim_paired.c
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Expand Up @@ -378,8 +378,8 @@ int paired_main(int argc, char *argv[]) {
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);
if (debug) fprintf(stderr, "p1cut: %d,%d\n", p1cut->five_prime_cut, p1cut->three_prime_cut);
if (debug) fprintf(stderr, "p2cut: %d,%d\n", p2cut->five_prime_cut, p2cut->three_prime_cut);

/* The sequence and quality print statements below print out the sequence string starting from the 5' cut */
/* and then only print out to the 3' cut, however, we need to adjust the 3' cut */
Expand Down Expand Up @@ -480,17 +480,17 @@ int paired_main(int argc, char *argv[]) {
}

if (!quiet) {
if (infn1 && infn2) fprintf(stdout, "\nPE forward 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);
if (infn1 && infn2) fprintf(stderr, "\nPE forward file: %s\nPE reverse file: %s\n", infn1, infn2);
if (infnc) fprintf(stderr, "\nPE interleaved file: %s\n", infnc);
fprintf(stderr, "\nTotal input FastQ records: %d (%d pairs)\n", total, (total / 2));
fprintf(stderr, "\nFastQ paired records kept: %d (%d pairs)\n", kept_p, (kept_p / 2));
if (pec) fprintf(stderr, "FastQ single records kept: %d\n", (kept_s1 + kept_s2));
else fprintf(stderr, "FastQ single records kept: %d (from PE1: %d, from PE2: %d)\n", (kept_s1 + kept_s2), kept_s1, kept_s2);

fprintf(stdout, "FastQ paired records discarded: %d (%d pairs)\n", discard_p, (discard_p / 2));
fprintf(stderr, "FastQ paired records discarded: %d (%d pairs)\n", discard_p, (discard_p / 2));

if (pec) fprintf(stdout, "FastQ single records discarded: %d\n\n", (discard_s1 + discard_s2));
else fprintf(stdout, "FastQ single records discarded: %d (from PE1: %d, from PE2: %d)\n\n", (discard_s1 + discard_s2), discard_s1, discard_s2);
if (pec) fprintf(stderr, "FastQ single records discarded: %d\n\n", (discard_s1 + discard_s2));
else fprintf(stderr, "FastQ single records discarded: %d (from PE1: %d, from PE2: %d)\n\n", (discard_s1 + discard_s2), discard_s1, discard_s2);
}

kseq_destroy(fqrec1);
Expand Down
4 changes: 2 additions & 2 deletions src/trim_single.c
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Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,7 @@ int single_main(int argc, char *argv[]) {
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);
if (debug) fprintf(stderr, "P1cut: %d,%d\n", p1cut->five_prime_cut, p1cut->three_prime_cut);

/* if sequence quality and length pass filter then output record, else discard */
if (p1cut->three_prime_cut >= 0) {
Expand All @@ -217,7 +217,7 @@ int single_main(int argc, char *argv[]) {
free(p1cut);
}

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);
if (!quiet) fprintf(stderr, "\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);
Expand Down