Security Policy¶

Reporting a Vulnerability¶

Send an E-mail to maintainer in private if vulnerabilities were found.

Known Bugs in `art_modern`¶

See News.md for details of the bugs fixed in each release.

Known Build-Time Incompatibilities¶

Clang earlier than 9 with Boost later than 1.78 may raise bug when using headers from boost/math as boost may misidentify Clang as GCC that does not support C++11. See here for more details.
Boost earlier than 1.65 does not contain boost/asio/thread_pool.hpp or boost/asio/post.hpp. See here for its first introduction. Under this circumstance, try -DUSE_THREAD_PARALLEL=BS in CMake options (introduced below) as an alternative.
GCC 13.3.0 on Haiku OS hrev58590 may generate a kernel panic that jam the entire system while building.
GCC would fail on Debian GNU/Hurd.
External HTSLib and NCBI NGS library incompatibilities: Both library defines string_dup.
Builds that uses Intel MKL or Intel C++/DPC++ compilers may be incompatible with Citrix Workspace app 25.08.10.111 under Linux.

Known Bugs in Original ART¶

Original ART may Produce Illegal SAM Files¶

Original ART Profile Builder Problem¶

The original ART profile builder would generate profiles with quality scores offset by 1.

Steps to reproduce:

Given file noqual_test/1.1.fq where qualities are all ! (Phred-score 0):

@1/1
AGCTAGCTAGCTAGCTAGCT
+
!!!!!!!!!!!!!!!!!!!!

and file noqual_test/1.2.fq:

@1/2
AGCTAGCTAGCTAGCTAGCT
+
!!!!!!!!!!!!!!!!!!!!

and file opt/noqual_test/ref.fa:

>a
AGCTAGCTACAGCTAGCTACAGCTAGCTACAGCTAGCTACAGCTAGCTACAGCTAGCTACTGATCG

Create a profile with command:

art_profiler_illumina opt/noqual_test/noqual_test_ opt/noqual_test fq

And then use the original ART to generate reads with the created profile:

art_illumina \
    --in opt/noqual_test/ref.fa \
    --out opt/noqual_test/art_out \
    --qprof1 opt/noqual_test/noqual_test_R1.txt \
    --rcount 2 --len 20 -amp --samout --maskN 0 --rndSeed 0

The generated file will look like:

@a-2
TGCGTATTCGGCCTTTGTTT
+
""""""""""""""""""""
@a-1
CGTAATTATACGCGCATGAG
+
""""""""""""""""""""

The qualities of generated file will be " (Phred-score 1), instead of ! (Phred-score 0) in the files where the profile is generated from.