ChangeLog

2019-05-12 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* migrated Shiny application

2018-10-10 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* major change (for latest RcppTOML) in database.toml and 
		related parameters name (. => _)

2018-09-26 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* fix cran check error

2018-06-04 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* update input UI when upload and delete files

2018-06-01 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add pipeline tabitem

2018-05-31 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Update Dockerfile and fix websocket connection
		* Opencpu package REST API

2018-05-24 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* fix download.database warning message (newest ini)

2018-05-23 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* support download/preview function for upload/output files

2018-05-22 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Support annotation module in shiny

2018-05-21 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Annotation tabitem UI
		* shiny tableout to DT tableout
		* vcfanno, vep, annovar change cmd 'print' to message
		* set solidHeader = FALSE in shiny box
		* add upload filetypes
		* improve input UI render method (render_input_box_ui)

2018-05-20 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* support background workers to process long time R commands
		* support clusterProfiler
		* auto update system monitor in dashbord page (10s)

2018-05-19 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add dashbord page in shiny app

2018-05-17 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add function check_shiny_dep
		* tryCatch for shiny app commands

2018-05-15 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* shiny APP support maftools demo plot with update function

2018-05-08 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* delete upload items supported in shiny APP 

2018-05-03 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add 2018sih_wgs_nkt_full_sqlite in normal pool

2018-02-26 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* initial anor shiny App (inst/extdata/tools/shiny)

2018-01-19 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* improve download.database for single 
		download.name and multiple version
		* add docm, intogen, disgenet and cancer_hotspots
		databases support

2018-01-18 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add returned colnames test

2018-01-17 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* fix a check bug in annovar

2018-01-06 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* R/annotation.R annotation.cols.match and 
		annotation.region.match added parameter fread.db.params

2018-01-05 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* 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 <lee_jianfeng@sjtu.edu.cn>

		* modified in dependence
		* change download.database parameters order

2017-12-15 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* 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 <lee_jianfeng@sjtu.edu.cn>

		* fix testthat 2.0 check error

2017-12-13 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* use ANNOVAR to annotate R object and input.file
		* dbscsnv11 be supported
		* add nastring paramter in annovar

2017-12-06 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* add tall_somatic_genes_201706

2017-12-05 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* 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 <lee_jianfeng@sjtu.edu.cn>

		* 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 <lee_jianfeng@sjtu.edu.cn>

		* 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 <lee_jianfeng@sjtu.edu.cn>

		* 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 <lee_jianfeng@sjtu.edu.cn>

		* b_all_rnaseq_v1_core and b_all_rnaseq_v1_extra be added

2017-11-29 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* hgnc_coding_gene2pre and hgnc_coding_pre2gene be supported
		* not show warnings in fread database step

2017-11-27 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* use do.call process external function 
		* document re-format
		* convert2annovar.pl be added in annovar

2017-11-26 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* sqlite.auto.build use split_row_file to 
		process big file
		* vignettes be added

2017-11-24 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Function annovar be added in R/external_tools.R

2017-11-23 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* CSCD database be supported
		* region match full tested
		* epi_genes_v1 be supported

2017-11-22 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Parallel and big.file mode be extract

2017-06-08 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* Download .sql file and convert to sqlite automatically

2017-06-07 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* sql2sqlite be added in R/build.R

2017-06-06 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* finished file check step be added

2017-06-05 Li Jianfeng <lee_jianfeng@sjtu.edu.cn>

		* 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 <lee_jianfeng@sjtu.edu.cn>
		
		* ANNOVAR databases download full supported
		* download.database use buildver
		* Unit test of download.database