Set the list of default BLAST output fields as suggested by @eparejatobes Fixed Any[Blast]OutputField new name Added totalReadsNumber output in the split loquat; and pass it as an input to the countint loquat Added frequency table to the counting loquat Renamed totalReadsNumber to mergedReadsNumber Added BLAST no-hits output Added merging for the no-hits chunks Added flash not-merged outputs Added a lot of crap to the MG7Parameters to make blast command configurable Added blastn as a default command Fixed blast for the case when the output is empty (create the empty output file) Fixed merge datamappings Removed merged reads count from the split step Added outputs with LCA/BBH-not-assigned read IDs Writing the whole no-hits read instead of just its header #44 Changed some data names; added .fa extension to the no-hits output Added a loquat that counts stats per each sample #9, #20 Added a loquat that merges sample-stats into a summary table #9, #20 Added a refined CSVFormat with \n line-ending and a shortcut for CSVWriter instantiation #48 Fixed also the CSVReader format Updated the loquat dep version #39 Moved some CSV-related things from the package object Some more advanced CSV trickery Added neccessary fields as implicits; it allows to make csv-select typesafe Migrated assignment code to the typesafe CSV-utils Made blast-filter predicate configurable; added default Updated to blast-api 0.7.0 Set blastn defaults to what was discussed with @eparejatobes and @rtobes #51 * Moved defaultBlastOutRec out of the package object Set up dependency on rnacentraldb; updated fastarious Using BlastDBRelease[AnyBlastDB] instead of the old AnyReferenceDB; removed old reference-db code (including GIs stuff) Removed bundles package; rearrenged related code Updated to rnacentral-0.2.1 Fixed two bugs causing this mysterious null problem: + the implicitly val for the argValsToSeq in the abstract AnyMG7Parameters trait. Even though the type for this implicitly[...] was fixed, it turned out to be null + the default predicate in the abstract trait had to be a lazy val (or a def) #53 Fixed assignment data-mapping (it doesn't need no-hits results) Removed not-assigned outputs, because they are always empty Fixed stats data mappings inputs Fixed input reads archive handling; it has to be uncompressed first Creating output file before trying to write to it Fixed summary step input Fixed the order of stats headers/values (Map mixes up the order) #55 Fixed FASTQ parsing in the stats step #55 Fixed the summary tasks and table #55 Interchanged assign and merge steps, so that assign is done in parallel per chunk #56 Removed unnecessary dependency overrides, commented out fat-jar settings Various fixes in the LCA algorithm and assignment data-mappings #47 Changed default Blast filter to (qcovs == 100 && gaps == 0); made gaps a mandatory field #57 Keep only the top BLAST hits #58 clean test sources rename src folders to match the package name