Fixed issues:

• #10, #11, #12, #13
• https://github.com/fritzsedlazeck/Spectre/issues/14 All contigs that are in the reference but now in coverage data are skipped, and a warning is issued. Furthermore, if no matching contigs are found, Spectre will terminate.
• https://github.com/fritzsedlazeck/Spectre/issues/15 Due to obsolete code references, Spectre would crash if provided with the --population flag in the CNVCaller mode. This has been updated accordingly.
• https://github.com/fritzsedlazeck/Spectre/issues/16 The flag --ploidy-chr required instructions on how to transform the chromosome coverage according to the global ploidy status. This has been changed only to provide the current ploidy state of the chromosome. Spectre will do the transformation calculation automatically now.
• https://github.com/fritzsedlazeck/Spectre/issues/17 When providing multiple samples without the --population flag, results have only been properly outputted to the first sample. Providing multiple samples has only been attended to be used with the --population flag. Thus, only CNVs will only be calculated for the first provided sample if the --population flag is missing.
• #20 GQ always showed the default score of the variant. This has been changed to show a phread like score. This score is based on a Z-score, which is used to determine how likely it is that the variant is a true variant. The SVSUPPORT flag was always visible even if no SNFJ file was used. This has been updated to be only present in the VCF if a SNFJ file has been used.
• Update Population mode:
  • Similarity merge of variant candidates
  • Reciprocal overlap, used to check only the smaller variant if they overlap by a certain percentage. Now it will check both variants if they overlap at least a certain percentage, e.g. 80%.

Further updates:

• Fixed: SPC file generation removed all values that were default values according to its datatype.
• Fixed: Re-initialization of variant candidates after loading the SPC file.
• Fixed: Updated functions that used paths only used in the debug mode.
• Added: Two new flags for the population mode --reciprocal-overlap and --disable-quality-filter:
  • --reciprocal-overlap will allow you to change the reciprocal overlap value when looking for the supporting variants in other samples.
  • --disable-quality-filter will allow you to look for supporting variants in the variants that did not pass the final filter of Spectre in the CNVCaller mode. (Non-passing reasons of the variants could have been that the variant was too small to pass the minimum CNV length, etc.)
• Added: Pre-calculation checks, which ensure that the user provides proper values.
• Added: Instructions on how to install the latest changes of Spectre locally with pip.
• Updated: Search for supporting variants is primarily done on variants that passed the final filter criteria of the CNVCaller mode.
• Updated: The minimum required package versions.
• Updated: Help message.
• Updated: README.md
• Updated: Minor code changes