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ChangeLog
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ChangeLog
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2017-01-06 Li Jianfeng <[email protected]>
* R/annotation.R annotation.cols.match and
annotation.region.match added parameter fread.db.params
2017-01-05 Li Jianfeng <[email protected]>
* added mysql.auto.build and mysql.auto.index
* supported external tools vep and vcfanno
* use vcfR package to parse VCF files to data.table object
2017-12-19 Li Jianfeng <[email protected]>
* modified in dependence
* change download.database parameters order
2017-12-15 Li Jianfeng <[email protected]>
* if os is windows set annovar.dir in PATH
* use annovar.anno.names when anno.name equal perl_annovar_merge
* download.database support multiple download.name
* improve test coverage
2017-12-14 Li Jianfeng <[email protected]>
* fix testthat 2.0 check error
2017-12-13 Li Jianfeng <[email protected]>
* use ANNOVAR to annotate R object and input.file
* dbscsnv11 be supported
* add nastring paramter in annovar
2017-12-06 Li Jianfeng <[email protected]>
* add tall_somatic_genes_201706
2017-12-05 Li Jianfeng <[email protected]>
* add set.db.sync.version and set.table.sync.version to get db and
table name (R/external_function.R)
2017-12-04 Li Jianfeng <[email protected]>
* fix start_index length error
* when skip != 0, the header set FALSE in fread (sqlite.auto.build)
* return.col.names.profix be support
2017-12-03 Li Jianfeng <[email protected]>
* optimize sqlite.auto.build
* add func get.annotation.needcols in R/get.R
* add param overwrite and append in sqlite.auto.build
2017-12-02 Li Jianfeng <[email protected]>
* download.database use default version
* update function annovar document
* download.database use download.name and download.cfg
* add function get.download.name
* dbname.fixed and table.name.fixed can be used in database.cfg
* new database be supoorted
* set function parameters default value
2017-11-30 Li Jianfeng <[email protected]>
* b_all_rnaseq_v1_core and b_all_rnaseq_v1_extra be added
2017-11-29 Li Jianfeng <[email protected]>
* hgnc_coding_gene2pre and hgnc_coding_pre2gene be supported
* not show warnings in fread database step
2017-11-27 Li Jianfeng <[email protected]>
* use do.call process external function
* document re-format
* convert2annovar.pl be added in annovar
2017-11-26 Li Jianfeng <[email protected]>
* sqlite.auto.build use split_row_file to
process big file
* vignettes be added
2017-11-24 Li Jianfeng <[email protected]>
* Function annovar be added in R/external_tools.R
2017-11-23 Li Jianfeng <[email protected]>
* CSCD database be supported
* region match full tested
* epi_genes_v1 be supported
2017-11-22 Li Jianfeng <[email protected]>
* Parallel and big.file mode be extract
2017-06-08 Li Jianfeng <[email protected]>
* Download .sql file and convert to sqlite automatically
2017-06-07 Li Jianfeng <[email protected]>
* sql2sqlite be added in R/build.R
2017-06-06 Li Jianfeng <[email protected]>
* finished file check step be added
2017-06-05 Li Jianfeng <[email protected]>
* MySQL db.type be supported
* build database from a file or a data.table object (R/build.R)
* dbname.fixed and table.name.fixed be added (R/annotation.R)
2017-06-04 Li Jianfeng <[email protected]>
* ANNOVAR databases download full supported
* download.database use buildver
* Unit test of download.database