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,
@@ -239,8 +237,12 @@ 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)
@@ -294,9 +296,6 @@ 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)