From b4d8e193cb89e56fafdf91ae94db7848b1a4b661 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Fri, 7 Aug 2026 18:47:33 -0700 Subject: [PATCH 1/2] src/simreads.cpp: setting default quality score to 63 (baseline of 33 plus 30?) so the simulated reads aren't flagged as poor quality --- src/simreads.cpp | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/simreads.cpp b/src/simreads.cpp index 2e67769..d8c4d75 100644 --- a/src/simreads.cpp +++ b/src/simreads.cpp @@ -78,9 +78,10 @@ rand_double() -> double { // ADS: in the interval [0, 1] } } // namespace simreads_random -static inline auto +[[nodiscard]] static inline auto format_fastq_record(const std::string &name, const std::string &read) -> std::string { + static constexpr auto assumed_quality_score = 63; assert(!name.empty()); std::string s; s += '@'; @@ -88,7 +89,7 @@ format_fastq_record(const std::string &name, s += '\n'; s += read; s += "\n+\n"; - s += std::string(std::size(read), 'B'); + s += std::string(std::size(read), assumed_quality_score); return s; } From ae9c01da10a6a08bf16b9d14dc4bd6e8e42187c1 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Fri, 7 Aug 2026 18:55:24 -0700 Subject: [PATCH 2/2] data/md5sum.txt: updating checksums for simulated test output fq files for changed default quality scores --- data/md5sum.txt | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/data/md5sum.txt b/data/md5sum.txt index a84c410..964ebaa 100644 --- a/data/md5sum.txt +++ b/data/md5sum.txt @@ -1,16 +1,16 @@ 46e60a92266ed0f913f5efb9b7c0473c tests/reads.sam -514bf940e7d5f44e57291a75e1fc6629 tests/reads_pe_1.fq -5487eb32b5492ddba3a95a8461e2ff4c tests/reads_pbat_pe_1.fq 57fd6ff3b49f4656c9506688040b7ce6 tests/tRex1.idx -64e17fc1e424f9cb21879d38ddf745e5 tests/reads_pe_2.fq -8bfa00acd0639dc66acd5aa8ac0369d5 tests/reads_rpbat_pe_2.fq 981dd110d1675c77533a485204fb13cc tests/reads.mstats 9b78ffb855d8a94604973118f2e19457 tests/reads_pbat_pe.sam a6a3a12238013d8081c3e06dd43d538c tests/reads_pe.sam a6e138f4b89ef2dc0b90004baadddb9b tests/reads_pbat_pe.mstats -aff19aeae4184c38cf364b3a94527098 tests/reads_pbat_pe_2.fq bd54ba1e720039cb4b662faa4f0e04b3 tests/reads_rpbat_pe.mstats d7a9e3f6a5ed7373a827f07aaf32803a tests/reads_pe.mstats -e94e71292fccd255bad3f3694efe7a4b tests/reads_rpbat_pe_1.fq -e95a8739a378bc5628c76ffbe8293682 tests/reads_1.fq edf2c97162f7910949520ed60d82f205 tests/reads_rpbat_pe.sam +d3c8f80d1c478f2be3477c366f563de0 tests/reads_1.fq +02decde770526f8545fa30514d717740 tests/reads_pbat_pe_1.fq +a8af19625ceae38dedf98a2d3496fd67 tests/reads_pbat_pe_2.fq +99de2ab83cd316abd986e5d89e135982 tests/reads_pe_1.fq +e6e7634b3d54d3362c1e6ec026783c70 tests/reads_pe_2.fq +005cab62b8f42d2d0fc856a7165422fd tests/reads_rpbat_pe_1.fq +900ebf83246886c1864635fbb5647b36 tests/reads_rpbat_pe_2.fq