[med-svn] [Git][med-team/falco][master] 4 commits: New upstream version 1.3.2
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Jun 11 11:42:34 BST 2026
Andreas Tille pushed to branch master at Debian Med / falco
Commits:
033dce3c by Andreas Tille at 2026-06-10T09:24:50+02:00
New upstream version 1.3.2
- - - - -
890ae025 by Andreas Tille at 2026-06-10T09:24:56+02:00
Update upstream source from tag 'upstream/1.3.2'
Update to upstream version '1.3.2'
with Debian dir 407ddcdcf524e0f2b32845b224efcebbe8aca946
- - - - -
33d7a8c2 by Andreas Tille at 2026-06-10T09:39:50+02:00
New upstream version
- - - - -
632399f0 by Andreas Tille at 2026-06-11T12:42:13+02:00
Close ITP bug
- - - - -
4 changed files:
- configure.ac
- debian/changelog
- src/StreamReader.cpp
- test/md5sum.txt
Changes:
=====================================
configure.ac
=====================================
@@ -14,7 +14,7 @@ dnl WITHOUT ANY WARRANTY; without even the implied warranty of
dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
dnl General Public License for more details.
-AC_INIT([falco], [1.3.1], [andrewds at usc.edu],
+AC_INIT([falco], [1.3.2], [andrewds at usc.edu],
[falco], [https://github.com/smithlabcode/falco])
dnl the config.h is not currently #included in the source, and only
dnl used to keep command lines short.
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-falco (1.3.1-1) UNRELEASED; urgency=medium
+falco (1.3.2-1) UNRELEASED; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #1139616)
-- Andreas Tille <tille at debian.org> Tue, 09 Jun 2026 16:26:08 +0200
=====================================
src/StreamReader.cpp
=====================================
@@ -692,27 +692,37 @@ FastqReader::~FastqReader() {
// Parses fastq gz by reading line by line into the gzbuf
bool
FastqReader::read_entry(FastqStats &stats, std::size_t &num_bytes_read) {
- cur_char = fgets(filebuf, RESERVE_SIZE, fileobj);
-
- // need to check here if we did not hit eof
+ cur_char = std::fgets(filebuf, RESERVE_SIZE, fileobj);
if (is_eof())
return false;
+ if (cur_char == nullptr)
+ throw std::runtime_error("encountered invalid read number: " +
+ std::to_string(stats.num_reads + 1));
do_read = (stats.num_reads == next_read);
read_tile_line(stats);
skip_separator();
- cur_char = fgets(filebuf, RESERVE_SIZE, fileobj);
+ cur_char = std::fgets(filebuf, RESERVE_SIZE, fileobj);
+ if (cur_char == nullptr)
+ throw std::runtime_error("encountered invalid read number: " +
+ std::to_string(stats.num_reads + 1));
read_sequence_line(stats);
skip_separator();
- cur_char = fgets(filebuf, RESERVE_SIZE, fileobj);
+ cur_char = std::fgets(filebuf, RESERVE_SIZE, fileobj);
+ if (cur_char == nullptr)
+ throw std::runtime_error("encountered invalid read number: " +
+ std::to_string(stats.num_reads + 1));
read_fast_forward_line();
skip_separator();
- cur_char = fgets(filebuf, RESERVE_SIZE, fileobj);
+ cur_char = std::fgets(filebuf, RESERVE_SIZE, fileobj);
+ if (cur_char == nullptr)
+ throw std::runtime_error("encountered invalid read number: " +
+ std::to_string(stats.num_reads + 1));
read_quality_line(stats);
skip_separator();
=====================================
test/md5sum.txt
=====================================
@@ -1,30 +1,30 @@
-6fb32514f5a67b6ac349be0747272495 test_output/SRR10143153_1/fastqc_data.txt
-9ad191925d47a57d4f8b12f21ba0a7c3 test_output/SRR10143153_1/summary.txt
-62ab46b4ce95b0cd76ecb9e72f7d7e3b test_output/SRR9624732_1/fastqc_data.txt
-c94f94bdfbed9b83f156c15ffea84127 test_output/SRR9624732_1/summary.txt
-8c080d1466e0b36b33067037f9edd2eb test_output/SRR3897196_2/fastqc_data.txt
-80cd130958bcb2219f1e5a07d06a3b6e test_output/SRR3897196_2/summary.txt
-16a1ba47dc2252f17ed3b763e6fd921d test_output/SRR10124060/fastqc_data.txt
+16e2812d1fb1503288517ad204d1d5f4 test_output/SRR10124060/fastqc_data.txt
776f7d1b53bbed8683de9ca1d2529f1e test_output/SRR10124060/summary.txt
-36c5ebf0b8f55a68e8eb9c73a16db8cf test_output/SRR3897196_1/fastqc_data.txt
-b736ee95d5c450ef5c0dda31957b6818 test_output/SRR3897196_1/summary.txt
-89bd71cceabbe7ba0b2da473eebf2890 test_output/SRR6387347/fastqc_data.txt
-a61f65047e76f93300967cf399d044de test_output/SRR6387347/summary.txt
-4c5c242c82f151f330ccc8d2b34b9d17 test_output/SRR1772703.lite.1/fastqc_data.txt
+d89e0e207fc4d1db79ea982281a920cd test_output/SRR10143153_1/fastqc_data.txt
+9ad191925d47a57d4f8b12f21ba0a7c3 test_output/SRR10143153_1/summary.txt
+6111e939668687d1b48b0faf3996f4af test_output/SRR10143153_2/fastqc_data.txt
+19f1811f324e4c44154f659bb6e22806 test_output/SRR10143153_2/summary.txt
+6869c2d401fc68790f03e0f44e70ab2c test_output/SRR1772703.lite.1/fastqc_data.txt
ad5727295e7c8de6eb6874837bf1518f test_output/SRR1772703.lite.1/summary.txt
-be1c33db6d105fab4f1d35142b7d3b66 test_output/SRR9878537.lite.1/fastqc_data.txt
-e5c40997d4993c07e164ee5598c39cf9 test_output/SRR9878537.lite.1/summary.txt
-0f0cb18c3d6b15301b00731a3d8694e9 test_output/SRR9624732_2/fastqc_data.txt
-fefc5d746f853c14b5e00421ad1ec260 test_output/SRR9624732_2/summary.txt
-b65e60aacf2c5aff868b725c77ee181d test_output/SRR1853178_2/fastqc_data.txt
-c331d0f7a6aa9d72be41ac531f9ba269 test_output/SRR1853178_2/summary.txt
-d86c1775f9bfff98343ceb93a712e63a test_output/SRR1853178_1/fastqc_data.txt
+8de8438185e7a4682b4f9def9efbd5b7 test_output/SRR1853178_1/fastqc_data.txt
36df1dcab539ba4ef885239fc8524636 test_output/SRR1853178_1/summary.txt
-198d1f368f19dd5b70bd8d63e083ee89 test_output/SRR10143153_2/fastqc_data.txt
-19f1811f324e4c44154f659bb6e22806 test_output/SRR10143153_2/summary.txt
-ee682b255b1d4824164b6a02878712dd test_output/SRR891268_2/fastqc_data.txt
-20a8e50baace4c672622793874a3d7de test_output/SRR891268_2/summary.txt
-44fdb71976ac47bd31c230fad841aa9e test_output/SRR891268_1/fastqc_data.txt
-69e7d0c53cd2e67117637c408b65333a test_output/SRR891268_1/summary.txt
-786295bff1d6169e3ef10dc4970c3a30 test_output/SRR6059706.lite.1/fastqc_data.txt
+fc0bfa1e0143ed06dda6999fbf5588aa test_output/SRR1853178_2/fastqc_data.txt
+c331d0f7a6aa9d72be41ac531f9ba269 test_output/SRR1853178_2/summary.txt
+8dc07f2b597a8866a9df84e3ebde0f38 test_output/SRR3897196_1/fastqc_data.txt
+b736ee95d5c450ef5c0dda31957b6818 test_output/SRR3897196_1/summary.txt
+21f6b1a9745e4f6fd9f74a3583fb93d7 test_output/SRR3897196_2/fastqc_data.txt
+80cd130958bcb2219f1e5a07d06a3b6e test_output/SRR3897196_2/summary.txt
+14b2a16b2ded1851605a9c5aaf30153a test_output/SRR6059706.lite.1/fastqc_data.txt
e348e4bcc7fc6f05e989ac7858d2b287 test_output/SRR6059706.lite.1/summary.txt
+5ffb8fadcd44cb08886e540871ad3267 test_output/SRR6387347/fastqc_data.txt
+a61f65047e76f93300967cf399d044de test_output/SRR6387347/summary.txt
+6a2d88378dbc961172fbf6dcc7a00339 test_output/SRR891268_1/fastqc_data.txt
+69e7d0c53cd2e67117637c408b65333a test_output/SRR891268_1/summary.txt
+485b013200cc99259d94aac50da9e48c test_output/SRR891268_2/fastqc_data.txt
+20a8e50baace4c672622793874a3d7de test_output/SRR891268_2/summary.txt
+35d6d130ca4423eb9b69b5f28129754d test_output/SRR9624732_1/fastqc_data.txt
+c94f94bdfbed9b83f156c15ffea84127 test_output/SRR9624732_1/summary.txt
+d3795756759b32243b7108ca84d3b5b5 test_output/SRR9624732_2/fastqc_data.txt
+fefc5d746f853c14b5e00421ad1ec260 test_output/SRR9624732_2/summary.txt
+4a12fd588b54713b5eed0d3ae334a99e test_output/SRR9878537.lite.1/fastqc_data.txt
+e5c40997d4993c07e164ee5598c39cf9 test_output/SRR9878537.lite.1/summary.txt
View it on GitLab: https://salsa.debian.org/med-team/falco/-/compare/f5edc7aa66c9c7dafc9cb5d1a935bd0ae6bd816b...632399f0a97865d25135e1e784247e0c10ec7bd1
--
View it on GitLab: https://salsa.debian.org/med-team/falco/-/compare/f5edc7aa66c9c7dafc9cb5d1a935bd0ae6bd816b...632399f0a97865d25135e1e784247e0c10ec7bd1
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