added support for alignment file indices in the {filename}.bai style preferred by picard

Author: jbelyeu

samplot/__init__.py

@@ -1,2 +1,2 @@
 #!/usr/bin/env python
-__version__ = "1.0.17"
+__version__ = "1.0.18"

samplot/samplot.py

@@ -2106,7 +2106,9 @@ def bam_file(bam):
             parser.error("alignment file {} is not in SAM/BAM/CRAM format".format(bam))
         idx_type = idx_options[options.index(ext)]
         #try the type-specific index name
-        if not os.path.isfile(bam + "." + idx_type):
+        picard_bam = os.path.splitext(bam)[0]
+        if (not os.path.isfile(bam + "." + idx_type) and 
+                not os.path.isfile(picard_bam + "." + idx_type)):
             idx_type = idx_options[3]
             #try the csi index name
             if not os.path.isfile(bam + "." + idx_type):