This is a minor update with a few bug fixes and one main feature improvement (parallel consensus sequence generation).
New features & bug fixes:
Script 1:
- Generation of consensus sequence is now parallel as the use of multiple threads for generating consensus sequences did not work efficiently. However, the process now uses all available cores. If only a single core is to be used the original version of the script is available as 1_generate_consensus_sequences_single-core.sh
- The intronerated contig sequences is now recovered and saved as not interleaved, which had caused issued for the merging in step 4
- The script now removes all text after the sample name in the fasta file, i.e. everything after the first space. HybPiper 2.0 does write information into the fasta files, which can lead to issues downstream.
Bugfixes:
Script 1a: The script hang up when an empty consensus file existed. Now a consensus file must have at least some content.
Script 1b: Fixed last line of file "2a_List_of_paralogs_removed_for_all_samples.txt" by adding end of line character
Script 1c: The removal of loci from sequence lists for intronerated /consensus did not work, but is fixed now.
Script 1c: Fixed bug that aborted sequence generation when there were failed loci
Script 3a: Correct generation of reference names when using intronerated contigs/consensus