Activity for Granger Sutton
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Granger Sutton committed [r166]
Allow genome names longer than 7 characters to be output in matrix files
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Made extend anchors more robust, allowed fewer CGNs for ends of contigs, reduced window sizes, and some other minor stuff
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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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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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fix hardcoding of max_mismatch in pull_seqs
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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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add ANI per cluster as last column of cluster_w...
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adjust create seed tuning for more diverse species
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Fix lack of symmetry in blast matches affecting...
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fixing a graph repair problem in the bubble smo...
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weight ANI/BSR distances by length of genes
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track counts for inserts
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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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resolving some incompatibilities between --appe...
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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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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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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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add support for multiple variant alleles in see...
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upgraded to blast+ seems to be a slight improve...
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correcting bug in calculation of pairwise BSR c...
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add R scripts for generating sample medoids as ...
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change rules for setting pairwise BSR cutoffs t...
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make scripts more tolerant of different syntax
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Tidy up options and add version
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Add some versioning options and move readme out...
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gene_order.pl added -L to usage and removed -L ...
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update gene_order.pl with some minor bug fixes
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Add starting from existing clusters, fix Jaccar...
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new plot R script
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update gene_order.pl and a few R scripts and ac...
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Add -R option to read precomputed clusters and ...
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Fix bug for uninitialized values when self matc...
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Fix bug to properly repair bubble when it has b...
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Add multiple new features to gene_order.pl, fix...
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Fixing some sort issues and output format and f...
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