Merge pull request #27 from genomewalker/reassign-disable-sort

Reassign disable sort

README.md

@@ -93,11 +93,11 @@ Full list of options:
 
 ```bash
 $ filterBAM reassign --help
-usage: filterBAM reassign [-h] --bam BAM [-p STR] [-r FILE] [-t INT] [-i INT] [-s FLOAT]
-                          [-A FLOAT] [-l INT] [-n INT] [--match-reward INT]
+usage: filterBAM reassign [-h] --bam BAM [-p STR] [-r FILE] [-t INT] [-i INT]
+                          [-s FLOAT] [-A FLOAT] [-l INT] [-n INT] [--match-reward INT]
                           [--mismatch-penalty INT] [--gap-open-penalty INT]
-                          [--gap-extension-penalty INT] [--lambda FLOAT] [-k FLOAT] [-o [FILE]]
-                          [-m STR] [-N] [--tmp-dir DIR]
+                          [--gap-extension-penalty INT] [--lambda FLOAT] [-k FLOAT]
+                          [-o [FILE]] [-m STR] [-N] [--tmp-dir DIR] [--disable-sort]
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -132,10 +132,13 @@ Re-assign optional arguments:
   -o [FILE], --out-bam [FILE]
                         Save a BAM file without multimapping reads (default: None)
   -m STR, --sort-memory STR
-                        Set maximum memory per thread for sorting; suffix K/M/G recognized
-                        (default: 1G)
+                        Set maximum memory per thread for sorting; suffix K/M/G
+                        recognized (default: 1G)
   -N, --sort-by-name    Sort by read names (default: False)
   --tmp-dir DIR         Temporary directory (default: None)
+
+miscellaneous arguments:
+  --disable-sort        Disable sorting of the filtered BAM file (default: False)
 ```
 
 

bam_filter/filter.py

@@ -93,6 +93,7 @@ def filter_references(args):
         mode="filter",
     )
 
+    sorted_bam = args.bam.replace(".bam", ".bf-sorted.bam")
     bam = check_bam_file(
         bam=args.bam,
         threads=4,
@@ -256,4 +257,12 @@ def filter_references(args):
 
     if args.low_memory:
         os.remove(out_files["bam_tmp_sorted"])
+    # check if sorted BAM file exists, if yes remove it
+    if os.path.exists(sorted_bam):
+        os.remove(sorted_bam)
+    # check if sorted BAM index file exists, if yes remove it
+    if os.path.exists(sorted_bam + ".bai"):
+        os.remove(sorted_bam + ".bai")
+    elif os.path.exists(sorted_bam + ".csi"):
+        os.remove(sorted_bam + ".csi")
     logging.info("ALL DONE.")