Update to v2.2.0

change_log.md

@@ -5,7 +5,7 @@
 - Add option `--end_with` to command `hybpiper assemble`. Allows the user to end the assembly pipeline at a chosen step (map_reads, distribute_reads, assemble_reads, exonerate_contigs).
 - Add option `--exonerate_skip_hits_with_frameshifts` to command `hybpiper assemble`. If provided, skip Exonerate hits where the SPAdes contig contains frameshifts when considering hits for assembly of an `*.FNA` sequence. Default behaviour in HybPiper v2.2.0 is to include these hits; previous versions allowed them automatically.
 - Add option `--exonerate_skip_hits_with_internal_stop_codons` to command `hybpiper assemble`. If provided, skip Exonerate hits where the SPAdes contig contains internal in-frame stop codon(s) when considering hits for assembly of an `*.FNA` sequence. A single terminal stop codon is allowed. Default behaviour in HybPiper v2.2.0 is to include these hits; previous versions allowed them automatically.  
-- Add option `--exonerate_skip_hits_with_terminal_stop_codons` to command `hybpiper assemble`. If provided, skip Exonerate hits where the SPAdes sequence contains a single terminal stop codon. Only applies when option "--exonerate_skip_hits_with_internal_stop_codons" is also provided. Only use this flag if your target file exclusively contains protein-coding genes with no stop codons included, and you would like to prevent any in-frame stop codons in the output sequences. Default behaviour in HybPiper v2.2.0 is to include these hits; previous versions allowed them automatically.
+- Add option `--exonerate_skip_hits_with_terminal_stop_codons` to command `hybpiper assemble`. If provided, skip Exonerate hits where the SPAdes sequence contains a single terminal stop codon. Only applies when option `--exonerate_skip_hits_with_internal_stop_codons` is also provided. Only use this flag if your target file exclusively contains protein-coding genes with no stop codons included, and you would like to prevent any in-frame stop codons in the output sequences. Default behaviour in HybPiper v2.2.0 is to include these hits; previous versions allowed them automatically.
 - Add option `--chimeric_stitched_contig_check` to command `hybpiper assemble`. If provided, HybPiper will attempt to determine whether a stitched contig is a potential chimera of contigs from multiple paralogs. Default behaviour in HybPiper v2.2.0 is to skip this check; previous versions performed the check automatically. Skipping this check speeds up the final 'exonerate_contigs' step of the pipeline, significantly.
 - Add option `--no_pad_stitched_contig_gaps_with_n` to command `hybpiper assemble`. If provided, when constructing stitched contigs, do not pad any gaps between hits (with respect to the "best" protein reference) with a number of Ns corresponding to the reference gap multiplied by 3. Default behaviour in HybPiper v2.2.0 is to pad gaps with Ns; previous versions did this automatically.
 - Add option `--skip_targetfile_checks` to command `hybpiper assemble`. Skip the target file checks. Can be used if you are confident that your target file has no issues (e.g. if you have previously run `hybpiper check_targetfile`).