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Enable canu bamoutput branch. Update Makefile to agree with latest, a…
…dd htslib, etc.
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Submodule canu
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+30 −2 | README.md | |
+36 −0 | scripts/build-all-compilers.sh | |
+3 −3 | src/Makefile | |
+6 −6 | src/Makefile.boilermake | |
+1 −1 | src/gfa/alignGFA.C | |
+1 −1 | src/haplotyping/splitHaplotype.C | |
+57 −11 | src/main.mk | |
+1 −1 | src/meryl | |
+16 −1 | src/overlapErrorAdjustment/findErrors-Output.C | |
+4 −4 | src/overlapInCore/edalign.C | |
+2 −1 | src/pipelines/canu.pl | |
+56 −13 | src/pipelines/canu/Consensus.pm | |
+44 −1 | src/pipelines/canu/Defaults.pm | |
+5 −3 | src/pipelines/canu/HaplotypeReads.pm | |
+1 −1 | src/seqrequester | |
+6 −1 | src/stores/sqCache.C | |
+1 −1 | src/stores/sqStoreCreate.C | |
+179 −33 | src/stores/tgTig.C | |
+22 −12 | src/stores/tgTig.H | |
+14 −13 | src/utgcns/layoutToPackage.C | |
+35 −3 | src/utgcns/libpbutgcns/AlnGraphBoost.C | |
+10 −4 | src/utgcns/libpbutgcns/AlnGraphBoost.H | |
+397 −489 | src/utgcns/unitigConsensus.C | |
+49 −50 | src/utgcns/unitigConsensus.H | |
+8 −6 | src/utgcns/utgcns-parameters.C | |
+31 −46 | src/utgcns/utgcns-processTigs.C | |
+61 −2 | src/utgcns/utgcns.C | |
+12 −0 | src/utgcns/utgcns.H | |
+4 −1 | src/utgcns/utgcns.mk | |
+1 −1 | src/utility |
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