From 90050458545cc14e3e27b7dac220c153c07c693e Mon Sep 17 00:00:00 2001
From: don <donkirkby@gmail.com>
Date: Wed, 12 Jul 2017 11:40:41 -0700
Subject: [PATCH] Stop sorting sam2aln to reduce memory usage for #393.

---
 micall/core/sam2aln.py | 32 +++++++++++++++++++++++---------
 1 file changed, 23 insertions(+), 9 deletions(-)

diff --git a/micall/core/sam2aln.py b/micall/core/sam2aln.py
index 7f9c267ec..380e8c501 100755
--- a/micall/core/sam2aln.py
+++ b/micall/core/sam2aln.py
@@ -14,6 +14,8 @@
 import re
 from multiprocessing.pool import Pool
 
+from micall.utils.big_counter import BigCounter
+
 SAM2ALN_Q_CUTOFFS = [15]  # Q-cutoff for base censoring
 MAX_PROP_N = 0.5                 # Drop reads with more censored bases than this proportion
 SAM_FLAG_IS_FIRST_SEGMENT = 0x40
@@ -434,6 +436,19 @@ def parse_sam_in_threads(remap_csv, nthreads, pair_processor):
         pool.join()
 
 
+class CounterFactory:
+    def __init__(self, aligned_file):
+        self.aligned_file_name = getattr(aligned_file, 'name', None)
+
+    def create_counter(self):
+        if self.aligned_file_name is None:
+            return Counter()
+        dirname = os.path.dirname(self.aligned_file_name)
+        file_prefix = os.path.join(os.path.abspath(dirname),
+                                   'merged_seq_counts')
+        return BigCounter(file_prefix=file_prefix)
+
+
 def sam2aln(remap_csv,
             aligned_csv,
             insert_csv=None,
@@ -468,7 +483,8 @@ def sam2aln(remap_csv,
         clipping_writer.writeheader()
 
     pair_processor = PairProcessor(is_clipping=clipping_csv is not None)
-    empty_region = defaultdict(Counter)
+    counter_factory = CounterFactory(aligned_csv)
+    empty_region = defaultdict(counter_factory.create_counter)
     aligned = defaultdict(empty_region.copy)  # {rname: {qcut: {mseq: count}}}
     if nthreads:
         regions = parse_sam_in_threads(remap_csv, nthreads, pair_processor)
@@ -477,7 +493,8 @@ def sam2aln(remap_csv,
         regions = map(pair_processor.process, matchmaker(remap_csv))
 
     for rname, mseqs, insert_list, failed_list in regions:
-        region = aligned[rname]
+        # noinspection PyTypeChecker
+        region = aligned[str(rname)]  # str() works around a PyCharm bug.
 
         for qcut, mseq in mseqs.items():
             # collect identical merged sequences
@@ -500,17 +517,14 @@ def sam2aln(remap_csv,
     aligned_writer = DictWriter(aligned_csv, aligned_fields, lineterminator=os.linesep)
     aligned_writer.writeheader()
     for rname in sorted(aligned.keys()):
-        data = aligned[rname]
-        for qcut, data2 in data.items():
-            # sort variants by count
-            intermed = [(count, len_gap_prefix(s), s) for s, count in data2.items()]
-            intermed.sort(reverse=True)
-            for rank, (count, offset, seq) in enumerate(intermed):
+        region = aligned[rname]
+        for qcut, mseq_counter in region.items():
+            for rank, (seq, count) in enumerate(mseq_counter.items()):
                 aligned_writer.writerow(dict(refname=rname,
                                              qcut=qcut,
                                              rank=rank,
                                              count=count,
-                                             offset=offset,
+                                             offset=len_gap_prefix(seq),
                                              seq=seq.strip('-')))