cblaster v1.3.19

What's Changed

• Checks for mistranslations in CDS annotations and truncated regions, other minor changes by @malanjary-wur in #94
• Update CITATION.cff with paper DOI by @althonos in #106

New Contributors

• @althonos made their first contribution in #106

Full Changelog: v1.3.18...v1.3.19

cblaster v1.3.18

• Fix NoneType error during result formatting (#90)
• Some bug fixes for stability (#87)

cblaster v1.3.17

• Fix off-by-one issues in extract_clusters module with intermediate genes (#83)
• Check for empty fields in IPG table (#85)

cblaster v1.3.16

• Fixes broken identical protein groups efetch request by setting db=ipg instead of db=protein (#84)
• Convert coordinates from IPG table to zero-based

cblaster v1.3.15

• Catch ValueError when parsing GFF sequence-region directive without coordinates
• Do not install genomicsqlite if installing cblaster on arm64

cblaster v1.3.14

• Fall back to built-in sqlite3 module when importing genomicsqlite fails

cblaster v1.3.13

Thanks to @brymerr921:

Bug fixes:

• By default, diamond blastp only saves a maximum of 25 hits per query, severely limiting the number of blast hits reported. Large databases are especially impacted. To solve this, the --hitlist_size is now passed on diamond inside cblaster search -m local. (1c16caa) (See issue #75)
• Added an option to cblaster makedb allowing users to provide a single txt file containing a list of input files. This solves the issue where the operating system limits the length of wildcard expansion on the command line. (bb9085c)
• Fixed error that arose when specifying sum or max for -bkey (fee315e) (see issue #76, thanks to @chasemc)

Enhancements:

• diamond makedb now uses the number of CPUs requested by the user (instead of all available CPUs) (0db55cc)

File compression:

• Use genomcsqlite3 to reduce the size of the final sqlite3 database by 40-60% (bae6b31)
• cblaster makedb accepts gzipped input files (241894d)
• cblaster makedb now writes a fasta.gz output file (241894d) and informs users they will need to decompress first if running hmmsearch (4c63fa5)

cblaster v1.3.12

• Fix extract_clusters module not working for HMM searches (2dcae87)

cblaster v1.3.11

• Explicitly check for decode method on HTTPResponse objects (as well as status code 200) from IPG Efetch to prevent AttributeError (#62)

cblaster v1.3.10

• Change default value for --percent argument to 0 from 50 to prevent confusion when no results
• Fix parsed GFF records not being correctly converted to SQL insertion tuples, should address #63