improve handling of cnseg file for different window sizes

README.md

@@ -250,8 +250,8 @@ Thickness of the arc qualitatively depicts the amount of paired-end read support
 The SV view file may be uploaded to web interface for Cycle view to visualize the cycles in conjunction with the SV view.
 
 
-### 5. [Intermediate] Copy number segmentation file `{out}_{CHROM}_{START}_{END}_cnseg.txt`
-This files provides the segmentation of an interval based on coverage alone. Here `{CHROM}_{START}_{END}` represent the coordinates of the interval. First line represents the header. Tab-separated fields:
+### 5. [Intermediate] Copy number segmentation file `{out}_{CHROM}_{START}_{END}_ws10000_cnseg.txt`
+This files provides the segmentation of an interval based on coverage alone. The value after `ws` indicates the window size used for the segmentation. Here `{CHROM}_{START}_{END}` represent the coordinates of the interval. First line represents the header. Tab-separated fields:
 - `{CHROM}`: Chromosome name
 - `{START}`: Coordinate of the first basepair in the segment
 - `{END}`: Coordinate of the last basepair in the segment

src/bam_to_breakpoint.py

@@ -751,8 +751,8 @@ def meanshift_refined(self, i, window_size0=10000, window_size1=300, gcc=False,
 
     def get_meanshift(self, i, window_size0=10000, window_size1=300, gcc=False):
         logging.debug("get_meanshift on " + str(i))
-        file_name = "%s_%s_%s_%s_cnseg.txt" % (self.sample_name, i.chrom, i.start, i.end)
-        if os.path.exists(file_name) and i.end - i.start > 50000:
+        file_name = "%s_%s_%s_%s_ws%s_cnseg.txt" % (self.sample_name, i.chrom, i.start, i.end, window_size0)
+        if os.path.exists(file_name) and i.end - i.start > 50000 and window_size0 == 10000:
             logging.debug("Re-using cn-seg info in " + file_name)
             msfile = open(file_name)
             msr = []