Changelog

v1.1.0 rpetit3/camlhmp "Wild Bactrian" 2024/08/25

`Added`

allow min-coverage and min-coverage params to be set in the yaml
- Priority:
  - user provided command line arguments (--min-pident and --min-coverage)
  - schema provided values
  - default values specified in the command script

v1.0.1 rpetit3/camlhmp "Bactrian" 2024/08/25

`Added`

camlhmp-blast-thresholds command to suggest specificity thresholds for BLAST results
print_versions to print versions from multiple schemas
print_camlhmp_version to print the camlhmp version

v1.0.0 rpetit3/camlhmp "Dromedary" 2024/08/15

`Added`

Added a mkdocs documentation site

`Fixed`

fixed camlhmp-blast-regions unnecessary debug output
fixed test schemas to match the new schema format

v0.3.1 rpetit3/camlhmp "Maybe a cat?" 2024/08/05

`Fixed`

camlhmp-blast-alleles not having a default value for targets

v0.3.0 rpetit3/camlhmp "More bunnies and fewer baby birds" 2024/08/05

`Added`

camlhmp-blast-alleles command to search alleles in a set of query sequences using BLAST algorithms

v0.2.2 rpetit3/camlhmp "Even a few baby birds" 2024/07/22

`Fixed`

--version flag now works as expected

v0.2.1 rpetit3/camlhmp "And a bunch of birds" 2024/07/22

`Added`

version output with schema name and version

`Fixed`

Empty input files will no longer be processed

v0.2.0 rpetit3/camlhmp "Four little bunnies" 2024/07/22

`Added`

camlhmp-blast-region command to search full regions of interest using BLAST algorithms
added camlhmp_version, schema_version, and params to output files

v0.1.0 rpetit3/camlhmp "Little baby legs" 2024/04/30

`Added`

camlhmp command to list all available commands
camlhmp-blast command to search for targets in a set of query sequences using BLAST algorithms
camlhmp-extract command to extract targets from a set of reference sequences
excludes field to types section to allow for exclusion of targets from a profile
replaced profiles section with types section to better reflect the schema structure
output of results for camlhmp-blast

v0.0.1 rpetit3/camlhmp "Not even walking yet" 2024/04/24

This is a development release for getting things on PyPi and Bioconda. Not expected to be stable.

`Added`

basics of camlhmp with a working example using partial SCCmec