### build track hubs for public SSMs data from aSHM reagions, pathologies BL, 

### DLBCL and FL, seq type genome and capture, projection grch37 and hg38

library(GAMBLR.utils)

library(GAMBLR.data)

library(dplyr)

# get metadata

my_meta = get_gambl_metadata(seq_type_filter = c("genome", "capture")) %>% 

  filter(pathology %in% c("BL", "DLBCL", "FL"))

# create hub for grch37

build_browser_hub(

  regions_bed = GAMBLR.data::grch37_ashm_regions,

  these_samples_metadata = my_meta,

  these_seq_types = c("genome", "capture"),

  projection = "grch37",

  local_web_host_dir = "~/repos/LLMPP",

  hub_dir = "hubs/ashm_hubs",

  splitColumnName = "pathology",

  hub_name = "gamblr_ashm", 

  shortLabel = "gamblr ashm", 

  longLabel = "GAMBLR public aSHM mutations from grch37 projection",

  contact_email = "rdmorin@sfu.ca"

)

# create hub for hg38

build_browser_hub(

  regions_bed = GAMBLR.data::hg38_ashm_regions,

  these_samples_metadata = my_meta,

  these_seq_types = c("genome", "capture"),

  projection = "hg38",

  local_web_host_dir = "~/repos/LLMPP",

  hub_dir = "hubs/ashm_hubs",

  splitColumnName = "pathology",

  hub_name = "gamblr_ashm", 

  shortLabel = "gamblr ashm", 

  longLabel = "GAMBLR public aSHM mutations from hg38 projection",

  contact_email = "rdmorin@sfu.ca"

)