From f82f789298bfb874d81b44ffbb5c90f860a31b68 Mon Sep 17 00:00:00 2001
From: Kishori M Konwar <43380010+kishorikonwar@users.noreply.github.com>
Date: Tue, 28 Jul 2020 13:59:50 -0400
Subject: [PATCH] Changed the intermediate files written during
 SplitBamByCellBarcodes from BAM to SAM (#79)

* changed the intermediate bam file writing of the SplitBam command to simply sam

* changed the intermediate bam file writing of the SplitBam command to simply sam
---
 src/sctools/bam.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/sctools/bam.py b/src/sctools/bam.py
index 8565d5a..d847738 100644
--- a/src/sctools/bam.py
+++ b/src/sctools/bam.py
@@ -325,11 +325,8 @@ def write_barcodes_to_bins(
         for i in range(len(bins)):
             out_bam_name = os.path.join(f"{dirname}", f"{dirname}_{i}.bam")
             filepaths.append(out_bam_name)
-            # For now, bam writing uses one thread for compression. Better logic could support more processes without
-            # starving the machine for resources
-            open_bam = pysam.AlignmentFile(
-                out_bam_name, "wb", template=input_alignments
-            )
+
+            open_bam = pysam.AlignmentFile(out_bam_name, "w", template=input_alignments)
             files.append(open_bam)
 
         # Loop over input; check each tag in priority order and partition barcodes into files based