Skip to content

Bugfix for malformed fastq file records and bumping version number for release #98

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
andrewdavidsmith merged 3 commits into from
Jun 9, 2026
+43 −33
Merged

Bugfix for malformed fastq file records and bumping version number for release #98

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
513da76
src/StreamReader.cpp: when reading fastq files, if an empty lines is …
andrewdavidsmith Jun 9, 2026
bc37dea
configure.ac: bumping patch version number for bugfix on malformed fa…
andrewdavidsmith Jun 9, 2026
6e12a8c
test/md5sum.txt: updating hashes for new version 1.3.2
andrewdavidsmith Jun 9, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion configure.ac
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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@usc.edu],
AC_INIT([falco], [1.3.2], [andrewds@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.
Expand Down
22 changes: 16 additions & 6 deletions src/StreamReader.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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();

Expand Down
52 changes: 26 additions & 26 deletions test/md5sum.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
Loading