khadi_dev

DESCRIPTION

@@ -17,7 +17,7 @@ Remotes:
   github::mskilab/gChain,
   github::mskilab/gGnome@0de9f45b5cf744375015ad4f164df555f05cf80a
 Depends:
-  R (>= 3.6.0),
+  R (>= 3.5.0),
   GenomicRanges,
   gUtils,
   gTrack,
@@ -41,4 +41,4 @@ Suggests:
   covr
 License: MIT + file LICENSE
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2

configure

@@ -1,5 +1,7 @@
 #!/bin/sh
 
+echo "configure working dir:"
+echo $(pwd)
 rm -rf src
 
 system=`uname`

inst/extdata/jba

@@ -1,4 +1,5 @@
 #!/usr/bin/env Rscript
+options(error = function() {traceback(2); quit('no',1)})
 library(optparse)
 jbastr = "
  _____         ___    _      _____ 
@@ -193,26 +194,37 @@ if (!exists("opt"))
             default = FALSE,
             help = "run filter.loose to get a breakdown of loose ends?"),
         make_option(
+            c("--max.threads"),
+            type = "integer",
+            default = 1L,
+            help = "run filter.loose to get a breakdown of loose ends?"),
             c("--gurobi"),
             type = "logical",
             default = FALSE,
             help = "use gurobi optimizer instead of CPLEX?"),
         make_option(c("-v", "--verbose"),
                     action = "store_true",
-                    default = FALSE,
+                    default = TRUE,
                     help = "verbose output")
     )
 
-    parseobj = OptionParser(usage = paste(c("jba JUNCTIONS COVERAGE [options]",
-                                            "\tJUNCTIONS can be BND style vcf, bedpe, rds of GrangesList",
-                                            " \tCOVERAGE is a .wig, .bw, .bedgraph, .bed., .rds of a granges, or .tsv  .csv /.txt  file that is coercible to a GRanges",
-                                            "\tuse --field=FIELD argument so specify which column to use if specific meta field of a multi-column table"),
-                                          collapse="\n"),
-                                          option_list=option_list)
-
-    args = tryCatch(parse_args(parseobj, positional_arguments= 2, print_help_and_exit = FALSE),
-                    error = function(e) {message(jbastr); print_help(parseobj); NULL})
+
+    parseobj = OptionParser(
+        usage = paste(
+            c("jba JUNCTIONS COVERAGE [options]",
+              "\tJUNCTIONS can be BND style vcf, bedpe, rds of GrangesList",
+              " \tCOVERAGE is a .wig, .bw, .bedgraph, .bed., .rds of a granges, or .tsv  .csv /.txt  file that is coercible to a GRanges",
+              "\tuse --field=FIELD argument so specify which column to use if specific meta field of a multi-column table"),
+            collapse="\n"),
+        option_list=option_list
+    )
+    args = tryCatch(
+        parse_args(parseobj,
+                   positional_arguments = TRUE,
+                   print_help_and_exit = FALSE),
 
+        error = function(e) {message(jbastr); print_help(parseobj); NULL}
+    )
 
     opt = NULL;
     if (!is.null(args)) {
@@ -223,6 +235,7 @@ if (!exists("opt"))
         {
             message('Did not find junction file ', opt$junctions)
             message('Warning: will be running JaBbA without junctions')
+            ## print_help(parseobj); stop()
             opt$junctions = ""
         }
         if (!file.exists(opt$coverage))
@@ -238,36 +251,42 @@ if (!exists("opt"))
 suppressPackageStartupMessages(
 {
 
-  if (!is.null(opt$seg) && is.character(opt$seg) && (is.na(opt$seg) || opt$seg == '/dev/null' || !file.exists(opt$seg)))
-  {
-    message('Did not find seg file ', opt$seg, ' setting to NULL')
-    opt$seg = NULL
-  }
+    if (!is.null(opt$seg) && is.character(opt$seg) && (is.na(opt$seg) || opt$seg == '/dev/null' || !file.exists(opt$seg)))
+    {
+        message('Did not find seg file ', opt$seg, ' setting to NULL')
+        opt$seg = NULL
+    }
+
 
+    ## if (!is.null(opt$j.supp) && (is.na(opt$j.supp) || opt$j.supp == '/dev/null' || !file.exists(opt$j.supp)))
+    ## {
+    ##   message('Did not find j.supp file ', opt$j.supp, ' setting to NULL')
+    ##   opt$j.supp = NULL
+    ## }
 
-  if (!is.null(opt$j.supp) && (is.na(opt$j.supp) || opt$j.supp == '/dev/null' || !file.exists(opt$j.supp)))
-  {
-    message('Did not find j.supp file ', opt$j.supp, ' setting to NULL')
-    opt$j.supp = NULL
-  }
+    if (!is.null(opt$hets) && (is.na(opt$hets) || opt$hets == '/dev/null' || !file.exists(opt$hets)))
+    {
+        message('Did not find hets file ', opt$hets, ' setting to NULL')
+        opt$hets = NULL
+    }
 
-  if (!is.null(opt$hets) && (is.na(opt$hets) || opt$hets == '/dev/null' || !file.exists(opt$hets)))
-  {
-    message('Did not find hets file ', opt$hets, ' setting to NULL')
-    opt$hets = NULL
-  }
+    if (!is.null(opt$nseg) && (is.na(opt$nseg) || opt$nseg == '/dev/null' || !file.exists(opt$nseg)))
+    {
+        message('Did not find nseg file ', opt$nseg, ' setting to NULL')
+        opt$nseg = NULL
+    }
 
-  if (!is.null(opt$nseg) && (is.na(opt$nseg) || opt$nseg == '/dev/null' || !file.exists(opt$nseg)))
-  {
-    message('Did not find nseg file ', opt$nseg, ' setting to NULL')
-    opt$nseg = NULL
-  }
+    if (!is.null(opt$j.supp) && (is.na(opt$j.supp) || opt$j.supp == '/dev/null' || !file.exists(opt$j.supp)))
+    {
+        message('Did not find supplementary junction file ', opt$j.supp, ' setting to NULL')
+        opt$j.supp = NULL
+    }
 
-  if (!is.null(opt$j.supp) && (is.na(opt$j.supp) || opt$j.supp == '/dev/null' || !file.exists(opt$j.supp)))
-  {
-    message('Did not find supplementary junction file ', opt$j.supp, ' setting to NULL')
-    opt$j.supp = NULL
-  }
+    if (!is.null(opt$blacklist.junctions) && (is.na(opt$blacklist.junctions) || opt$blacklist.junctions == '/dev/null' || !file.exists(opt$blacklist.junctions)))
+    {
+        message('Did not find blacklist.junctions file ', opt$blacklist.junctions, ' setting to NULL')
+        opt$blacklist.junctions = NULL
+    }
 
 
     require(JaBbA)
@@ -317,6 +336,7 @@ suppressPackageStartupMessages(
         loose.penalty.mode = ifelse(opt$linear, "linear", "boolean"),
         tilim = opt$tilim,
         epgap = opt$epgap,
+        max.threads = opt$max.threads,
         use.gurobi = opt$gurobi,
         ## TODO max.threads = Inf, max.mem = 16
         ## below are general options
@@ -328,9 +348,8 @@ suppressPackageStartupMessages(
         ism = opt$ism,
         verbose = 2,
         fix.thres = opt$fix.thres,
-        filter_loose = opt$filter_loose
+        filter_loose = opt$filter_loose,
+        rescue.all = opt$rescue.all
     )
 })
-
-
-
+quit('no', 0)