FAQ on fastqrab documentationhttps://tyberiusprime.github.io/fastqrab/main/docs/faq/Recent content in FAQ on fastqrab documentationHugoen-us<link>https://tyberiusprime.github.io/fastqrab/main/docs/faq/trouble_shooting/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://tyberiusprime.github.io/fastqrab/main/docs/faq/trouble_shooting/</guid><description><h1 id="troubleshooting"> Troubleshooting <a class="anchor" href="#troubleshooting">#</a> </h1> <h2 id="i-dont-know-what-to-do-after-an-error-message"> I don&rsquo;t know what to do after an error message <a class="anchor" href="#i-dont-know-what-to-do-after-an-error-message">#</a> </h2> <p>Well, that&rsquo;s below our targets, we want our error messages to tell you enough for you to be able to fix it.</p> <p>Please file a bug report in our <a href="https://github.com/tyberiusPrime/fastqrab/issues">issue tracker</a>.</p> <h2 id="i-received-a-friendly-panic-message"> I received a friendly panic message <a class="anchor" href="#i-received-a-friendly-panic-message">#</a> </h2> <p>These look like this</p> <div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>Well, this is embarrassing. </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>fastqrab had a problem and crashed. To help us diagnose the problem you can send us a crash report. </span></span><span style="display:flex;"><span> </span></span><span style="display:flex;"><span>We have generated a report file at <span style="color:#e6db74">&#34;/tmp/nix-shell.ty6dWk/report-89ffc0f3-8076-4f55-83f0-c0a5d2fb3b55.toml&#34;</span>. </span></span></code></pre></div><p>This kind of error message, which wraps a rust &lsquo;panic&rsquo; only happens if fastqrab has managed to get into an impossible or unforeseen state.</p></description></item><item><title/><link>https://tyberiusprime.github.io/fastqrab/main/docs/faq/changelog/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://tyberiusprime.github.io/fastqrab/main/docs/faq/changelog/</guid><description><h1 id="changelog"> Changelog <a class="anchor" href="#changelog">#</a> </h1> <h2 id="v090"> v0.9.0 <a class="anchor" href="#v090">#</a> </h2> <h3 id="general"> General <a class="anchor" href="#general">#</a> </h3> <ul> <li>Renamed project from mbf-fastq-processor to fastqrab</li> <li>Much improved error messages pinpointing exactly what needs to change.</li> </ul> <h3 id="new--renamed-steps"> New &amp; renamed steps <a class="anchor" href="#new--renamed-steps">#</a> </h3> <ul> <li>New step: ConcatTags — concatenate multiple tags into one</li> <li>New step: Lowercase — unified replacement for LowercaseTag/LowercaseSequence</li> <li>New step: SpotCheckReadPairing — Hamming-distance based read pairing validation</li> <li>New step: ExtractIUPACSuffix added</li> <li>OtherFile unified: OtherFileByName and OtherFileBySequence merged into one step</li> <li>ExtractAnchor merged into ExtractRegions</li> <li>NCount -&gt; NContent to be inline with GCContent</li> <li>NContent/GCContent now support (and require) relative (counts or rate?)</li> </ul> <h3 id="step-changes"> Step changes <a class="anchor" href="#step-changes">#</a> </h3> <ul> <li>Conditional Swap/ReverseComplement variants merged into the main steps</li> <li><a href="https://tyberiusprime.github.io/fastqrab/main/fastqrab/main/docs/concepts/tag/#conditional-processing">if tag</a> support on 8 core editing steps for conditional read editing</li> <li>ExtractIUPAC: multiple queries in one step, max_mismatches now required, large performance improvements</li> <li>min_length added to ExtractRegionsOfLowQuality</li> <li>Quality checking added to Prefix/Postfix</li> <li>Tag replacement within regular expressions</li> </ul> <h3 id="output-changes"> Output changes <a class="anchor" href="#output-changes">#</a> </h3> <ul> <li>Tag histogram reports; demultiplex data nested under &lsquo;demultiplex&rsquo; key in reports</li> </ul> <h3 id="performance"> Performance <a class="anchor" href="#performance">#</a> </h3> <ul> <li>Redesigned multi-core engine: workpool based, better controllable, better documented</li> <li>Default thread count now uses all available CPU cores</li> <li>Rapidgzip for parallel gzip decompression, now also for FASTA; auto-detected; included in Nix builds</li> <li>Arena-based parsers for FASTA and BAM</li> <li>Parallel BAM decoding</li> <li>Multicore EvalExpression, ReportCountOligos, ReportLengthDistribution</li> <li>Prefix/Postfix massively improved performance</li> <li>Merge base statistics ~80% faster</li> <li>ConcatTags ~15% faster</li> <li>IUPAC matching: replaced Sassy with optimized pure-Rust implementation</li> <li>Optimized SwapConditional, TrimAtTag, StoreTagBackInSequence, FilterReservoirSample, Rename</li> <li>Dynamic cuckoo filter sizing; initial_filter_capacity documented; read count estimation</li> </ul> <h3 id="other"> Other <a class="anchor" href="#other">#</a> </h3> <ul> <li>verify command: validates a pipeline produces expected output; auto-detects config, captures stdout/stderr</li> <li>configuration toml can now be read from stdin (incompatible with reads from stdin).</li> <li>Shell autocompletion for bash, fish, and zsh</li> <li>benchmark mode and per-step benchmark harness</li> <li>template command: shows help on error</li> <li>LLM configuration guide and template.toml rewrite for LLM-assisted config generation</li> <li>TagLabel type: all tag names are now strongly typed; duplicate tag names produce a clear error</li> <li>IndexMap replaces HashMap everywhere for deterministic output order</li> <li>unwrap() replaced with expect() throughout; clippy::unwrap_used now denied</li> <li>MSRV pinned to match flake.nix Rust version</li> <li>Security: upgraded bytes crate (GHSA-434x-w66g-qw3r)</li> <li>Upgraded dependencies</li> </ul> <h3 id="documentation"> Documentation <a class="anchor" href="#documentation">#</a> </h3> <ul> <li>Four new cookbooks for common FastQ processing tasks</li> <li>Copy-to-clipboard button in docs</li> <li>Documentation URLs included in validation failure messages</li> <li>Added mascot</li> </ul> <h3 id="bug-fixes"> Bug fixes <a class="anchor" href="#bug-fixes">#</a> </h3> <ul> <li>Fixed fastp merge algorithm (replaced with direct port of the reference C++ algorithm)</li> <li>Fixed invalid FASTQ detection when comment line doesn&rsquo;t start with &lsquo;+&rsquo;</li> <li>Fixed Windows newline detection edge case in parser</li> <li>Fixed Local-Local FastQElement swap</li> <li>Fixed demultiplex &amp; fragment count in reports</li> <li>Fixed Head short-circuit (broken by SpotCheckReadPairing)</li> <li>Fixed ignore_unaligned → now include_mapped / include_unmapped</li> <li>Fixed barcode overlapping multiple matches</li> </ul> <h2 id="v081"> v0.8.1 <a class="anchor" href="#v081">#</a> </h2> <ul> <li>Github release workflow test</li> </ul> <h2 id="v080"> v0.8.0 <a class="anchor" href="#v080">#</a> </h2> <ul> <li>Versioned documentation</li> <li>First revision where very major feature is in place. Changelog starts here.</li> </ul></description></item></channel></rss>