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v1.2.1: performance, clustering, C++17 modernization

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@hamidamz hamidamz released this 06 Apr 16:09
· 2 commits to main since this release
v1.2.1
a1b35a7
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Learn about vigilant mode.

Performance

  • Replaced kseq++ (C++ wrapper) with kseq.h (Heng Li) for faster sequence I/O (~13% speedup in querysketch)
  • Batch-read pattern in querySample eliminates per-read lock contention under OpenMP
  • Rolling hash in lowComplexity filter replaces per-position recomputation
  • Stack-allocated spectrum arrays in lowComplexity replace heap-allocated vectors
  • Replaced std::endl with "\n" in hot loops to avoid unnecessary stream flushes
  • BloomFilter constructor uses value-initialized allocation instead of manual zeroing
  • comparesketch pre-caches all k-mer hashes to avoid redundant file I/O (M+N reads instead of M×N)
  • comparesketch reuses per-thread Bloom filters with memset instead of re-allocating
  • Sort lambda and range-for loops use const references to avoid copies

Features

  • Genomically spaced signature selection in buildSketch — signatures are evenly distributed across reference genome positions instead of randomly shuffled
  • Added read-level log output (logread_*.tsv) in querysketch listing matched read IDs per reference
  • comparesketch now supports compressed FASTA input (.fa.gz) via kseq.h/zlib
  • Added CMake build system (CMakeLists.txt) alongside existing Makefile
  • Added --cluster=N option to uniqsketch: automatically clusters nearly identical references using single-linkage union-find on pairwise unique k-mer counts, selects a representative per cluster, and outputs clusters.tsv mapping all members to their representatives

Error Handling

  • Added file existence validation for all input files across all three tools
  • Typo'd filenames now produce clear error messages instead of core dumps
  • Missing @list files are caught before processing
  • Bloom filter error message now reports k-mer counts, k value, and suggests causes/fixes
  • Empty lines in list files are skipped

Code Quality

  • Modern C++17 style throughout: nullptr, using aliases, static_cast, structured bindings
  • Removed using namespace std from headers (BloomFilter.hpp, ntcard.hpp)
  • All headers are self-contained with explicit includes
  • Fixed typo: identifyDiffernce → identifyDifference
  • Fixed version string bug in querysketch ("querysketch1.1.0" → "querysketch Version 1.1.0")
  • Fixed signed/unsigned comparison warnings in readCutoff checks
  • Consistent Doxygen-style documentation on all public functions
  • Removed unused b2c lookup table from SequenceUtil.hpp
  • Simplified getBaseId to handle edge cases (no slash, no extension, multiple dots)

Tests

  • Added comparesketchtest: loadBloomFilter, checkBloomFilter (identical and different references)
  • Added BloomFilter tests: empty filter, get_pop, store/load roundtrip
  • Extended getBaseId tests: multiple dots, no extension, no directory separator
  • Total: 15 tests across 4 test suites (up from 9 across 3)

Dependencies

  • Replaced kseq++ (kseq++.hpp, seqio.hpp, config.hpp) with kseq.h from seqtk
  • Updated THIRD-PARTY-LICENSES accordingly

Contributors

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