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Update readme for 2.0.2 Test #223: Commit 81c394b pushed by bede
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Default map-ont preset now implicit rather than explicit, permitting … Test #222: Commit e87e82c pushed by bede
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Bump changelog for 2.0.1 Test #221: Commit f4af206 pushed by bede
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2.0.1: fix for breaking change in defopt 7.0.0 Test #220: Commit 8e99caa pushed by bede
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Remove recently problematic gawk dep from conda deps, readme trivia Test #219: Commit ff0ff44 pushed by bede
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Describe alignment parameters and how to override them Test #218: Commit 6c859c2 pushed by bede
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Describe --aligner-args, warn about increasing FPR Test #217: Commit 4469e04 pushed by bede
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Add basic workflow diagram Test #216: Commit 1e16f4a pushed by bede
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Add basic workflow diagram Test #215: Commit 07cc5ec pushed by bede
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Readme typos, CLI help formatting Test #214: Commit 3ec85a0 pushed by bede
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Mention stdout in fastq1 fastq2 CLI help, readme intro Test #213: Commit 0aa3a52 pushed by bede
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2.0.0 release detail Test #212: Commit b024e7b pushed by bede
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New index-related subcommands Test #211: Commit 2f601cd pushed by bede
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Changelog structure Test #210: Commit 53f7290 pushed by bede
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Add changelog Test #209: Commit 622aef5 pushed by bede
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68 tests passing Test #208: Commit fec40c6 pushed by bede
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Support stdin for Bowtie2 (Minimap2 not yet passing test Test #207: Commit f6ef634 pushed by bede
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Rename --offline to --airplane to free up -o for --output Test #206: Commit d3045aa pushed by bede
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Support stdin for single/unpaired reads with --fastq1 - Test #205: Commit b07f7d8 pushed by bede
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Support CASAVA 1.8+ style headers (--casava) #41 Test #204: Commit c71e024 pushed by bede
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Support CASAVA 1.8+ style headers (--casava) #41 Test #203: Commit eb83fa5 pushed by bede
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Partial support for CASAVA 1.8+ style headers (--casava) #41 Test #202: Commit dd5d6bb pushed by bede
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Paired read stdout example Test #201: Commit 0d47ee2 pushed by bede
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Smart thread count allocation between alignment and compression Test #200: Commit 637e387 pushed by bede
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Error msg for mismatched read counts, update log output for stdout, test Test #199: Commit 493b44a pushed by bede
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