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Published April 22, 2016 | Version v1.0.0-M3-fair-lca-top-hits
Software Open

mg7: mg7 v1.0.0-M3-fair-lca-top-hits

Authors/Creators

  • 1. Era7 Bioinformatics
  • 2. oh no sequences! - Era7 bioinformatics
  • 3. ohnosequences!, Era7 Bioinformatics
  • 4. Gitter

Description

  • 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

Files

mg7-v1.0.0-M3-fair-lca-top-hits.zip

Files (6.7 MB)

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Additional details

Related works

Is supplement to
https://github.com/ohnosequences/mg7/tree/v1.0.0-M3-fair-lca-top-hits (URL)