remove deprecated "max_reads_in_ram_per_tile" from picard opts, expos…

…e opt "sort" (#71)

comment out deprecated "max_reads_in_ram_per_tile" from picard opts, expose opt sort, also re-enable Intel compression

tools/picard.py

@@ -46,7 +46,7 @@ def execute(self, command, picardOptions=None, JVMmemory=None, background=False,
 
         # the conda version wraps the jar file with a shell script
         path = self.install_and_get_path()
-        tool_cmd = [path, '-Xmx' + JVMmemory, '-Djava.io.tmpdir=' + tempfile.gettempdir(), command] + picardOptions + ['USE_JDK_DEFLATER=true','USE_JDK_INFLATER=true']
+        tool_cmd = [path, '-Xmx' + JVMmemory, '-Djava.io.tmpdir=' + tempfile.gettempdir(), command] + picardOptions # + ['USE_JDK_DEFLATER=true','USE_JDK_INFLATER=true']
         _log.debug(' '.join(tool_cmd))
 
         env = os.environ.copy()
@@ -491,16 +491,19 @@ class IlluminaBasecallsToSamTool(PicardTools):
     defaults = {
         'read_structure': '101T8B8B101T',
         'adapters_to_check': ('PAIRED_END', 'NEXTERA_V1', 'NEXTERA_V2'),
-        'max_reads_in_ram_per_tile': 1000000,
+        # MAX_READS_IN_RAM_PER_TILE is deprecated in newer versions of Picard in favor of MAX_RECORDS_IN_RAM
+        # commenting out for now until fully removed from picard
+        #'max_reads_in_ram_per_tile': 1000000, 
         'max_records_in_ram': 2000000,
         'num_processors': 0,
         'include_non_pf_reads': False,
         'compression_level': 7,
+        'sort': True
     }
     option_list = (
-        'read_structure', 'sequencing_center', 'adapters_to_check', 'platform', 'max_reads_in_ram_per_tile',
+        'read_structure', 'sequencing_center', 'adapters_to_check', 'platform',
         'max_records_in_ram', 'num_processors', 'apply_eamss_filter', 'force_gc', 'first_tile', 'tile_limit',
-        'include_non_pf_reads', 'run_start_date', 'read_group_id', 'compression_level'
+        'include_non_pf_reads', 'run_start_date', 'read_group_id', 'compression_level', 'sort'
     )
 
     # pylint: disable=W0221
@@ -529,6 +532,10 @@ def execute(self,
             'BASECALLS_DIR=' + basecalls_dir, 'BARCODES_DIR=' + barcodes_dir, 'LANE=' + str(lane),
             'RUN_BARCODE=' + read_group_id_precursor, 'LIBRARY_PARAMS=' + library_params
         ]
+        # MAX_READS_IN_RAM_PER_TILE is deprecated in newer versions of Picard in favor of MAX_RECORDS_IN_RAM
+        # remove from opts; this list comprehension can be removed once MAX_READS_IN_RAM_PER_TILE is removed
+        # from picard
+        opts = [opt for opt in opts if "MAX_READS_IN_RAM_PER_TILE" not in opt]
         PicardTools.execute(self, self.subtoolName, opts, JVMmemory)
 
     def execute_single_sample(self,