Activity for LOCUST
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Erin Beck committed [r102]
new round of multi-copy to correctly print ST files and work with novel flag
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initial commit of multi copy work
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bug fix with duplicate alleles
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added --input_path option
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fixed bugs
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auxiliary script to make non redundant multifasta files to allow for use as an allele file in LOCUST
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added publication to help
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point CURRENT tag to 2.0
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Release now includes increment option as well as HMM searching
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updating to current version
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updated missing options from help documentation
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added the no_dos2unix flag
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forgot to commit required scripts
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fixed parameter error
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new version to run core hmm checker
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initial add of HMM core checks
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Added stdout capturing of tophits in order to create a log file
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removed log file. Will add better logging in the future
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Granger Sutton committed [r84]
Modified selection of seeds to be less restrictive on possibly poorly trimmed alleles. Changed best hits to prefer full length matches over bitscore. Modified hash reference to avoid warning message. Added two overalp cases for allele check which shouldn't actually change behavior but is more correct.
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modified that if alleles overlap that only the allele with the larger bitscore is kept as the true hit.
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Fixed: Append schema was not calling NEW/NOVEL ...
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modified it to only count genomes where blast h...
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fixed non showing alleles in novel schema printing
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changed novel allele to use allele list from se...
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fixed header issue, causing skipping of genomes
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updated tree building to not fail if files don'...
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updated error messaging and handling
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updated error messages and handling
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fixing last fix continue/next
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change zero length Blast results from ERROR to ...
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check that hash is defined before calling keys
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fixed paths to point to correct location of res...
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fixed output file locations between previous an...
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added increment option
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added log file to mention when a genome/allele ...
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updated copyright statement
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LOCUST released /User Manual.pdf
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Tagging current release as 1.0
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Tagging current release as 1.0
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added license disclaimer
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moved mac config to main area and adding dos2un...
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changed order of when files get cleaned up
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added biosample_list as user input to be run th...
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program now runs dos2unix on user input as a ch...
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now calls raxmlHPC directly and not raxmlFasta
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added sys call for mac call for raxmlHPC
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added wide character fix
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mac specific executables
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added mac executables
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removed final alignment step
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changed shebang lines
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fix hardcoding of max_mismatch in pull_seqs
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removed problem steps in raxmlFasta that are no...
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made file name more descriptive
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fixed the download type option
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fixed function call
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newer version of script
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bug fix
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Fixed options for ftp downloaded. Also modified...
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Fix create seed for no redundant allele case
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Correct set cover algorithm for seed creation a...
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Fixed cutFasta to call local installation
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fixed the script to not re-copy sequences downl...
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updated file names of appended schema files to ...
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updating to fix duplicate index scheme
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adjust create seed tuning for more diverse species
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changed output file names to work for ftp downl...
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committing Jason's fix of using curl for the do...
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updated parameters for ftp downloader. Made cre...
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added muscle to config file and modified tree_b...
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adding necessary scripts for tree building
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improve create_seed allele sanity checks
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fix minor bug in WARNING message
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Added checks to create_seed code to look for al...
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Adding local version to checkout. Also modified...
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addining additonal modules needed for tree buil...
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resolving some incompatibilities between --appe...
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adding modified version of ftp downloader
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Allow all attributes in the schema file to be a...
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Fixed bug in overlapping match check to include...
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Enhanced code to allow etra columns in schema a...
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added config option to typer. Allows user to mo...
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adding cleanFasta to be included in checkout
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added lib directory with modules needed for cle...
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Check for overlapping matches to different gene...
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Added more sanity checks for alleles and schema...
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Fixing an edge case for --create_seed where non...
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Improving handling of NOVEL alleles for --appen...
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Fix novel allele naming for appended alleles
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add support for _# in allele names to tree buil...
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fix minor file name error
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added --tree option to typer. modified paramete...
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checking in Pratap's tree building code as a st...
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Adding help for --creat_seed option
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Adding --creat_seed for creating a seeds file f...
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fix bug in append_schema I introduced in refact...
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fix some bugs in append_schema mode
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