remove low_memory

README.md

@@ -568,11 +568,9 @@ We recommend _not_ to modify these options unless you are clearly aware of their
  for storing the annotation database, because SQLite database cannot be created on a shared disks.
  The folder will be created automatically.
 
-`--low_memory`
- Deprecated, default behaviour since 3.2.
-
 `--high_memory`
- Cache read alignments instead for making several passes over a BAM file, noticeably increases RAM usage.
+ Cache read alignments instead for making several passes over a BAM file, noticeably increases RAM usage, 
+but may improve running time when disk I/O is relatively slow.
 
 `--min_mapq`
  Filers out all alignments with MAPQ less than this value (will also filter all secondary alignments, as they typically have MAPQ = 0).

isoquant.py

@@ -185,8 +185,6 @@ def add_hidden_option(*args, **kwargs): # show command only with --full-help
  help="align reads to reference without running further analysis")
 
  # ADDITIONAL
- add_additional_option("--low_memory", help="decrease RAM consumption (deprecated, set by default)",
- action='store_true', default=True)
  add_additional_option("--high_memory", help="increase RAM consumption (store alignment and the genome in RAM)",
  action='store_true', default=False)
  add_additional_option("--no_junc_bed", action="store_true", default=False,
@@ -239,11 +237,13 @@ def add_hidden_option(*args, **kwargs): # show command only with --full-help
  type=str, required=True)
  resume_parser.add_argument('--debug', action='store_true', default=argparse.SUPPRESS,
  help='Debug log output.')
- resume_parser.add_argument("--threads", "-t", help="number of threads to use", type=int, default=argparse.SUPPRESS)
- resume_parser.add_argument("--low_memory", help="decrease RAM consumption (deprecated, set by default)",
+ resume_parser.add_argument("--threads", "-t", help="number of threads to use",
+ type=int, default=argparse.SUPPRESS)
+ resume_parser.add_argument("--high_memory",
+ help="increase RAM consumption (store alignment and the genome in RAM)",
+ action='store_true', default=False)
+ resume_parser.add_argument("--keep_tmp", help="do not remove temporary files in the end",
  action='store_true', default=argparse.SUPPRESS)
- resume_parser.add_argument("--keep_tmp", help="do not remove temporary files in the end", action='store_true',
- default=argparse.SUPPRESS)
  args, unknown_args = resume_parser.parse_known_args(sys.argv[1:])
  if unknown_args:
  logger.error("You cannot specify options other than --output/--threads/--debug/--low_memory "
@@ -294,9 +294,6 @@ def check_and_load_args(args, parser):
  elif not os.path.exists(args.genedb_output):
  os.makedirs(args.genedb_output)
 
- if args.high_memory:
- args.low_memory = False
-
  if not check_input_params(args):
  parser.print_usage()
  exit(-1)

src/alignment_processor.py

@@ -229,7 +229,7 @@ def __init__(self, chr_id, bam_pairs, params, illumina_bam, genedb=None, chr_rec
 
  self.bam_merger = BAMOnlineMerger(self.bam_pairs, self.chr_id, 0,
  self.bam_pairs[0][0].get_reference_length(self.chr_id),
- multiple_iterators=self.params.low_memory)
+ multiple_iterators=not self.params.high_memory)
  self.strand_detector = StrandDetector(self.chr_record)
  self.read_groupper = read_groupper
  self.polya_finder = PolyAFinder(self.params.polya_window, self.params.polya_fraction)
@@ -238,7 +238,7 @@ def __init__(self, chr_id, bam_pairs, params, illumina_bam, genedb=None, chr_rec
 
  def process(self):
  current_region = None
- alignment_storage = BAMAlignmentStorage(self.bam_merger) if self.params.low_memory else InMemoryAlignmentStorage()
+ alignment_storage = BAMAlignmentStorage(self.bam_merger) if not self.params.high_memory else InMemoryAlignmentStorage()
 
  for bam_index, alignment in self.bam_merger.get():
  if alignment_storage.alignment_is_not_adjacent(alignment):

src/dataset_processor.py

@@ -90,7 +90,7 @@ def set_polya_requirement_strategy(flag, polya_requirement_strategy):
 
 def collect_reads_in_parallel(sample, chr_id, args):
  current_chr_record = Fasta(args.reference)[chr_id]
- if not args.low_memory:
+ if args.high_memory:
  current_chr_record = str(current_chr_record)
  read_grouper = create_read_grouper(args, sample, chr_id)
  lock_file = reads_collected_lock_file_name(sample.out_raw_file, chr_id)