v1.6.1

Minor changes

• Makes all read counting dependent on args.verbose #112

v1.6.0

Minor changes

• Enhancement:
  • Allow compiling with newer gcc versions (up to gcc 9.1) #86
  • Use Bioconda to distribute MATAM #5
  • Better dependencies checking #43 #82 #83 #84
  • Be more explicit when a command using runner module fails #55
• Various bug fix:
  • Check properly the return code of system calls for sub-scripts #91
  • Better error management with multiprocessing pool #81 #92
  • Check the encoding of FASTQ file #89
  • Remove the support of FASTA file as input #93

v1.5.3

Minor changes

• Be less stringent when filtering RDP results #67

v1.5.2

Minor changes

• Fix a bug when parsing RDP results #61
• Expose RDP cutoff #59

v1.5.1

Minor changes

• Bug fix: when the RDP confidence threshold (at genus level) is under a threshold of 0.8, then tag all taxonomic nodes as "unclassified" #58
• Standardize RDP taxa #39
• Integrate travis for CI #57

v1.5.0

Major changes

• Allow dynamic reduction of the coverage for highly covered references #34

Minor changes

• Clean up logging system and redirect logs to a file #26
• Allow to resume from taxonomic_assignment step #50
• Replace the fatal error by a warning for scaffolds with abundance equal to zero #29
• Update SGA to the last version
• Various bug fix:
  • Docker build errors #44 #46
  • Missing symlink #51

v1.4.0

Major changes

• Add a script to compare taxonomic assignments from multiple datasets #41

Minor changes

• Improve output files visibility #22
• Make the krona tabulated file an output file #30
• Expose the min scaffold length as a parameter #35

v1.3.0

Major changes

• The components assembly step has been parallelized #8
• A new correction mode has been added to the components assembly step #12
• Make easier the integration of a new assembler for the components assembly step #24

v1.2.1

Minor changes

• Improve files naming #21
• Update docker file to fix missing dependency #20
• Raise an error when Getting no scaffold > 500bp #19
• Fix a bug in RDP parsing #23

v1.2.0

Major changes

• Compute abundance for each scaffolds
• Perform taxonomic assignment with RDP classifier
• Allow the hierarchical data visualization with Krona