[med-svn] [Git][med-team/sickle][master] 8 commits: Use git mode in watch file to include some interesting commits after latest release
Andreas Tille
gitlab at salsa.debian.org
Wed Oct 24 18:57:15 BST 2018
Andreas Tille pushed to branch master at Debian Med / sickle
Commits:
0dc260cf by Andreas Tille at 2018-10-24T17:28:18Z
Use git mode in watch file to include some interesting commits after latest release
- - - - -
70b5efe2 by Andreas Tille at 2018-10-24T17:28:45Z
New upstream version 1.33+git20150314.f3d6ae3
- - - - -
f0478a3c by Andreas Tille at 2018-10-24T17:28:45Z
Update upstream source from tag 'upstream/1.33+git20150314.f3d6ae3'
Update to upstream version '1.33+git20150314.f3d6ae3'
with Debian dir de2c18bb2a68b82378f8b354fba2a530718a4aaa
- - - - -
dbebeab6 by Andreas Tille at 2018-10-24T17:29:35Z
debhelper 11
- - - - -
890e9319 by Andreas Tille at 2018-10-24T17:29:38Z
Point Vcs fields to salsa.debian.org
- - - - -
3464b627 by Andreas Tille at 2018-10-24T17:29:38Z
Standards-Version: 4.2.1
- - - - -
49d16157 by Andreas Tille at 2018-10-24T17:31:45Z
hardening=+all
- - - - -
08d86087 by Andreas Tille at 2018-10-24T17:32:16Z
Upload to unstable
- - - - -
11 changed files:
- Makefile
- README.md
- debian/changelog
- debian/compat
- debian/control
- debian/rules
- debian/watch
- sickle.xml
- src/kseq.h
- src/trim_paired.c
- src/trim_single.c
Changes:
=====================================
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
=====================================
@@ -1,3 +1,14 @@
+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 at 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
=====================================
@@ -1 +1 @@
-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
=====================================
@@ -1,5 +1,7 @@
#!/usr/bin/make -f
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
%:
dh $@
=====================================
debian/watch
=====================================
@@ -1,3 +1,7 @@
-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
=====================================
@@ -191,7 +191,12 @@ typedef struct __kstring_t {
} \
} \
if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
- seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
+ 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 */ \
seq->qual.m = seq->seq.m; \
=====================================
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);
View it on GitLab: https://salsa.debian.org/med-team/sickle/compare/824a60eac3edb096c24bdf195dbe8e2955593717...08d860870c801f19a2928ef15dd5cee0b8625e99
--
View it on GitLab: https://salsa.debian.org/med-team/sickle/compare/824a60eac3edb096c24bdf195dbe8e2955593717...08d860870c801f19a2928ef15dd5cee0b8625e99
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