Get AlignmentSet by SL system and Job Id

smrtlinkJobResolver.R

#!/usr/bin/env Rscript

# ls /pbi/dept/secondary/siv/smrtlink/smrtlink-*
ALPHA <- "alpha"
BETA <- "beta"
BIHOURLY <- "bi-hourly"
NIGHLTLY <- "nightly"
SIV <- "siv"
SIV_ALPHA <- "siv-alpha"


.getRootJobsDir <- function(smrtLinkId) {
  return(paste0("/pbi/dept/secondary/siv/smrtlink/smrtlink-", smrtLinkId, "/smrtsuite/userdata/jobs_root"))
}

.toJobDir <- function(rootDir, jobId) {
  prefix <- floor(jobId / 1000)
  return(paste(rootDir, sprintf("%03d", prefix), sprintf("%06d", jobId), sep="/"))
}

getAlignmentSetPath <- function(smrtlinkId, jobId) {
  pattern <- paste0(.toJobDir(.getRootJobsDir(smrtlinkId), jobId), "/tasks/*/final*alignmentset.xml")
  return(Sys.glob(pattern))
}


main <- function() {
  jobId <- 4367
  cat(paste("Running example for job", jobId, "on SMRT Link system", BETA, "\n"))
  alignmentSetPath <- getAlignmentSetPath(BETA, jobId)
  cat(paste("Results ", alignmentSetPath, "\n"))
  # expected output
  # mkocher@login14-biofx01:~$ ./smrtlinkJobResolver.R
  # Running example for job 4367 on SMRT Link system beta 
  # Results  /pbi/dept/secondary/siv/smrtlink/smrtlink-beta/smrtsuite/userdata/jobs_root/004/004367/tasks/pbalign.tasks.consolidate_bam-0/final.alignmentset.alignmentset.xml
  return(0)
}

q(status = main())