head 1.4; access; symbols pkgsrc-2023Q4:1.4.0.6 pkgsrc-2023Q4-base:1.4 pkgsrc-2023Q3:1.4.0.4 pkgsrc-2023Q3-base:1.4 pkgsrc-2023Q2:1.4.0.2 pkgsrc-2023Q2-base:1.4 pkgsrc-2023Q1:1.1.0.34 pkgsrc-2023Q1-base:1.1 pkgsrc-2022Q4:1.1.0.32 pkgsrc-2022Q4-base:1.1 pkgsrc-2022Q3:1.1.0.30 pkgsrc-2022Q3-base:1.1 pkgsrc-2022Q2:1.1.0.28 pkgsrc-2022Q2-base:1.1 pkgsrc-2022Q1:1.1.0.26 pkgsrc-2022Q1-base:1.1 pkgsrc-2021Q4:1.1.0.24 pkgsrc-2021Q4-base:1.1 pkgsrc-2021Q3:1.1.0.22 pkgsrc-2021Q3-base:1.1 pkgsrc-2021Q2:1.1.0.20 pkgsrc-2021Q2-base:1.1 pkgsrc-2021Q1:1.1.0.18 pkgsrc-2021Q1-base:1.1 pkgsrc-2020Q4:1.1.0.16 pkgsrc-2020Q4-base:1.1 pkgsrc-2020Q3:1.1.0.14 pkgsrc-2020Q3-base:1.1 pkgsrc-2020Q2:1.1.0.12 pkgsrc-2020Q2-base:1.1 pkgsrc-2020Q1:1.1.0.8 pkgsrc-2020Q1-base:1.1 pkgsrc-2019Q4:1.1.0.10 pkgsrc-2019Q4-base:1.1 pkgsrc-2019Q3:1.1.0.6 pkgsrc-2019Q3-base:1.1 pkgsrc-2019Q2:1.1.0.4 pkgsrc-2019Q2-base:1.1 pkgsrc-2019Q1:1.1.0.2 pkgsrc-2019Q1-base:1.1; locks; strict; comment @# @; 1.4 date 2023.05.20.14.42.11; author bacon; state Exp; branches; next 1.3; commitid 8RILFeKtJELCaIpE; 1.3 date 2023.05.20.11.27.27; author bacon; state Exp; branches; next 1.2; commitid dYMeBtIFfV0k5HpE; 1.2 date 2023.05.18.18.17.32; author bacon; state Exp; branches; next 1.1; commitid n0kkHuV914heqtpE; 1.1 date 2019.01.07.02.33.17; author bacon; state Exp; branches; next ; commitid HfnComiKFLAHnN6B; desc @@ 1.4 log @biology/canu: Fix build on Darwin aarch64 Replace SIMDE with upstream source hacks from FreeBSD port Should also work on powerpc, but untested No changes to existing binaries @ text @@@comment $NetBSD$ bin/alignGFA bin/bogart bin/canu bin/canu-time bin/canu.defaults bin/correctOverlaps bin/draw-tig bin/dumpBlob bin/edalign bin/errorEstimate bin/falconsense bin/filterCorrectionLayouts bin/filterCorrectionOverlaps bin/findErrors bin/findErrors-Dump bin/fixErrors bin/generateCorrectionLayouts bin/layoutReads bin/loadCorrectedReads bin/loadErates bin/loadTrimmedReads bin/mergeRanges bin/meryl bin/mhapConvert bin/mmapConvert bin/ovStoreBucketizer bin/ovStoreBuild bin/ovStoreConfig bin/ovStoreDump bin/ovStoreIndexer bin/ovStoreSorter bin/ovStoreStats bin/overlapAlign bin/overlapCheck bin/overlapConvert bin/overlapImport bin/overlapInCore bin/overlapInCorePartition bin/overlapPair bin/prefixEditDistance-matchLimitGenerate bin/splitHaplotype bin/splitReads bin/sqStoreCreate bin/sqStoreDumpFASTQ bin/sqStoreDumpMetaData bin/tgStoreCompress bin/tgStoreDump bin/tgStoreLoad bin/tgTigDisplay bin/trimReads bin/utgcns lib/perl5/site_perl/canu/Configure.pm lib/perl5/site_perl/canu/Consensus.pm lib/perl5/site_perl/canu/CorrectReads.pm lib/perl5/site_perl/canu/Defaults.pm lib/perl5/site_perl/canu/Execution.pm lib/perl5/site_perl/canu/Grid.pm lib/perl5/site_perl/canu/Grid_Cloud.pm lib/perl5/site_perl/canu/Grid_DNANexus.pm lib/perl5/site_perl/canu/Grid_LSF.pm lib/perl5/site_perl/canu/Grid_Local.pm lib/perl5/site_perl/canu/Grid_PBSTorque.pm lib/perl5/site_perl/canu/Grid_SGE.pm lib/perl5/site_perl/canu/Grid_Slurm.pm lib/perl5/site_perl/canu/HaplotypeReads.pm lib/perl5/site_perl/canu/Meryl.pm lib/perl5/site_perl/canu/Output.pm lib/perl5/site_perl/canu/OverlapBasedTrimming.pm lib/perl5/site_perl/canu/OverlapErrorAdjustment.pm lib/perl5/site_perl/canu/OverlapInCore.pm lib/perl5/site_perl/canu/OverlapMMap.pm lib/perl5/site_perl/canu/OverlapMhap.pm lib/perl5/site_perl/canu/OverlapStore.pm lib/perl5/site_perl/canu/Report.pm lib/perl5/site_perl/canu/SequenceStore.pm lib/perl5/site_perl/canu/Unitig.pm share/java/classes/mhap-2.1.3.jar @ 1.3 log @biology/canu: Hacks to support Darwin x86 OpenMP support needs improvement Darwin aarch64 still blocked by glib2 build issues No changes to binaries on other platforms @ text @@ 1.2 log @biology/canu: Update to 2.2 Numerous new features, enhancements, and bug fixes since 1.8 Enabled support for aarch64 May work on other 64-bit platforms, but untested Changes: https://github.com/marbl/canu/releases @ text @@ 1.1 log @biology/canu: import canu-1.8 Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence consensus Trim corrected sequences Assemble trimmed corrected sequences @ text @a3 1 bin/bogus d5 2 d8 1 a12 4 bin/fastqAnalyze bin/fastqSample bin/fastqSimulate bin/fastqSimulate-sort d17 1 d19 1 d23 1 d34 2 a41 2 bin/readConsensus bin/sequence a44 1 bin/sqStoreCreatePartition a47 1 bin/tgStoreCoverageStat a48 1 bin/tgStoreFilter a52 1 bin/wtdbgConvert d62 1 @