ganon version 1.0.0 #181
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ganon version 1.0.0 #181
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* version 1.0.0 * added seqan3 as module, compiling on cmake, working * building with Seqan3 * working classify * working with wrappers * test ssh connection * pull seqan3 * seqan2 removed * tests python passing, fixing cpp test * cpp tests build passing * remove bkp files * test working, but not passing. Small differences in counting * remove sdsl-lite lib cmake * remove include sdsl * fix test, disable offset tests * fix files test * remove incompatible test travis * better agent and hash * better parsing reads * update seqan3.1.0 * format * offset with views * fix print uint8_t * fix missing sum paired * fixed threshold calculation * fix min-kmers threshold calculation * validate 0 min_kmers * improve build code * auto type hashes to compile gcc7
* new cpp tests ganon-build * more tests build and update * remove data files ganon-build tests * remove copy cmake, add missing file
* io ganon-build, automatic bin per file * improved code ganon-build and auto bin generation working * default output rep, optional lca output * option to output lca on python side * one kmer size per hierarchical level * working without map and tax * code improv. * fixed map size with auto bins * fix tests
* Report per threads, without atomic int * stats reporting unique * count unique without lca, better print stats * fix copy filters function validate_targets_tax * fix stats float * better stats struct, account for skipped reads
* new classify tests cpp * remove files test classify, do not copy over cmake * more tests ganon-classify * added test tax * more tests classify, output in folders * adding tests classify with errors * more tests with errors * more tests * more tests
* validate input files * error msg * generalized filesystem import via seqan3
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ganon version 1.0.0
ganon-build:
ganon-classify: