Makefile

@@ -35,7 +35,7 @@ distclean: clean
 	rm -rf *.tar.gz
 
 dist:
-	tar -zcf $(ARCHIVE).tar.gz src Makefile
+	tar -zcf $(ARCHIVE).tar.gz src Makefile README.md sickle.xml LICENSE
 
 build: sliding.o trim_single.o trim_paired.o sickle.o print_record.o
 	$(CC) $(CFLAGS) $(LDFLAGS) $(OPT) $? -o sickle $(LIBS)

README.md

@@ -94,6 +94,7 @@ truncation of sequences with Ns.
     sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -q 33 -l 40
     sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq -x -n
     sickle se -t sanger -g -f input_file.fastq -o trimmed_output_file.fastq.gz
+    sickle se --fastq-file input_file.fastq --qual-type sanger --output-file trimmed_output_file.fastq
 
 ### Sickle Paired End (`sickle pe`)
 
@@ -134,3 +135,7 @@ enable truncation of sequences with Ns.
     -s trimmed_singles_file.fastq.gz
 
     sickle pe -c combo.fastq -t sanger -M combo_trimmed_all.fastq
+
+    sickle pe --pe-file1 input_file1.fastq --pe-file2 input_file2.fastq --qual-type sanger \
+    --output-pe1 trimmed_output_file1.fastq --output-pe2 trimmed_output_file2.fastq \
+    --output-single trimmed_singles_file.fastq

debian/changelog

+sickle (1.33+git20150314.f3d6ae3-1) unstable; urgency=medium
+
+  * Use git mode in watch file to include some interesting commits
+    after latest release
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * hardening=+all
+
+ -- Andreas Tille <tille@debian.org>  Wed, 24 Oct 2018 19:31:53 +0200
+
 sickle (1.33-2) unstable; urgency=medium
 
   * Moved packaging from SVN to Git

debian/compat

-10
+11

debian/control

@@ -6,10 +6,10 @@ Section: science
 Priority: optional
 Build-Depends: zlib1g-dev,
                help2man,
-               debhelper (>= 10)
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sickle.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/sickle.git
+               debhelper (>= 11~)
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/sickle
+Vcs-Git: https://salsa.debian.org/med-team/sickle.git
 Homepage: https://github.com/najoshi/sickle
 
 Package: sickle

debian/rules

 #!/usr/bin/make -f
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 %:
 	dh $@
 

debian/watch

-version=3
+version=4
 
-https://github.com/najoshi/sickle/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+opts="mode=git,pretty=1.33+git%cd.%h" \
+    https://github.com/najoshi/sickle.git HEAD
+
+# some interesting commits were done after latest release
+# https://github.com/najoshi/sickle/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)

sickle.xml

@@ -69,7 +69,6 @@
 		-n
 		#end if
 
-		--quiet
 	</command>
 
 	<inputs>

src/kseq.h

@@ -191,6 +191,11 @@ typedef struct __kstring_t {
    }                                                                    \
    }                                                                    \
      if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
+     if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
+     seq->seq.m = seq->seq.l + 2; \
+     kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
+     seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
+     } \
      seq->seq.s[seq->seq.l] = 0;    /* null terminated string */    \
      if (c != '+') return seq->seq.l; /* FASTA */                       \
      if (seq->qual.m < seq->seq.m) {	/* allocate enough memory */	\

src/trim_paired.c

@@ -18,20 +18,20 @@ int paired_length_threshold = 20;
 
 static struct option paired_long_options[] = {
     {"qual-type", required_argument, 0, 't'},
-    {"pe-file1", optional_argument, 0, 'f'},
-    {"pe-file2", optional_argument, 0, 'r'},
-    {"pe-combo", optional_argument, 0, 'c'},
-    {"output-pe1", optional_argument, 0, 'o'},
-    {"output-pe2", optional_argument, 0, 'p'},
-    {"output-single", optional_argument, 0, 's'},
-    {"output-combo", optional_argument, 0, 'm'},
-    {"qual-threshold", optional_argument, 0, 'q'},
-    {"length-threshold", optional_argument, 0, 'l'},
-    {"no-fiveprime", optional_argument, 0, 'x'},
-    {"truncate-n", optional_argument, 0, 'n'},
-    {"gzip-output", optional_argument, 0, 'g'},
-    {"output-combo-all", optional_argument, 0, 'M'},
-    {"quiet", optional_argument, 0, 'z'},
+    {"pe-file1", required_argument, 0, 'f'},
+    {"pe-file2", required_argument, 0, 'r'},
+    {"pe-combo", required_argument, 0, 'c'},
+    {"output-pe1", required_argument, 0, 'o'},
+    {"output-pe2", required_argument, 0, 'p'},
+    {"output-single", required_argument, 0, 's'},
+    {"output-combo", required_argument, 0, 'm'},
+    {"qual-threshold", required_argument, 0, 'q'},
+    {"length-threshold", required_argument, 0, 'l'},
+    {"no-fiveprime", no_argument, 0, 'x'},
+    {"truncate-n", no_argument, 0, 'n'},
+    {"gzip-output", no_argument, 0, 'g'},
+    {"output-combo-all", required_argument, 0, 'M'},
+    {"quiet", no_argument, 0, 'z'},
     {GETOPT_HELP_OPTION_DECL},
     {GETOPT_VERSION_OPTION_DECL},
     {NULL, 0, NULL, 0}
@@ -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 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);

src/trim_single.c

@@ -19,12 +19,12 @@ static struct option single_long_options[] = {
     {"fastq-file", required_argument, 0, 'f'},
     {"output-file", required_argument, 0, 'o'},
     {"qual-type", required_argument, 0, 't'},
-    {"qual-threshold", optional_argument, 0, 'q'},
-    {"length-threshold", optional_argument, 0, 'l'},
-    {"no-fiveprime", optional_argument, 0, 'x'},
-    {"discard-n", optional_argument, 0, 'n'},
-    {"gzip-output", optional_argument, 0, 'g'},
-    {"quiet", optional_argument, 0, 'z'},
+    {"qual-threshold", required_argument, 0, 'q'},
+    {"length-threshold", required_argument, 0, 'l'},
+    {"no-fiveprime", no_argument, 0, 'x'},
+    {"discard-n", no_argument, 0, 'n'},
+    {"gzip-output", no_argument, 0, 'g'},
+    {"quiet", no_argument, 0, 'z'},
     {GETOPT_HELP_OPTION_DECL},
     {GETOPT_VERSION_OPTION_DECL},
     {NULL, 0, NULL, 0}
@@ -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);