https://github.com/makaho/kallisto
Tip revision: aae8e515ba794480ebc1580931a058216de585f7 authored by Pall Melsted on 26 October 2015, 10:05:39 UTC
Adds secondary flag to pseudobam to play nice with other tools
Adds secondary flag to pseudobam to play nice with other tools
Tip revision: aae8e51
test_index.cpp
#include "catch.hpp"
#include "common.h"
#include "KmerIndex.h"
#include "KmerIterator.hpp"
#include <string>
#include <stdio.h>
// TEST_CASE("Build index", "[build_index]")
// {
//
// ProgramOptions global_opts, local_opts;
// std::string short_trans {"../test/input/10_trans_gt_500_bp.fasta"};
//
// global_opts.k = 21;
//
// // TODO: figure out a better way to deal with initialization
// Kmer::set_k(global_opts.k);
//
// KmerIndex kidx(global_opts);
// kidx.BuildTranscripts(short_trans);
// kidx.write("tmp.idx");
//
//
//
// local_opts.index = "tmp.idx";
// local_opts.k = 0;
// KmerIndex jidx(local_opts);
// jidx.load(local_opts);
//
//
// remove("tmp.idx");
//
// REQUIRE( kidx.k == local_opts.k );
// REQUIRE( kidx.k == jidx.k );
// REQUIRE( kidx.num_trans == jidx.num_trans );
// REQUIRE( kidx.kmap.size() == jidx.kmap.size() );
// REQUIRE( kidx.ecmap.size() == jidx.ecmap.size() );
//
// // TODO: write tests to compare actual maps
// }