incorporated recent changes from master

src/hatchet/utils/cluster_bins.py

@@ -85,7 +85,12 @@ def readBB(bbfile):
                     read[chromosome, start, end].append((sample, rd, snps, cov, alpha, beta, baf))
                 except KeyError:
                     read[chromosome, start, end] = [(sample, rd, snps, cov, alpha, beta, baf)]
-    return read, samples
+    nonzeroab = (lambda rb : all(rec[4] + rec[5] > 0 for rec in rb))
+    newread = {b : read[b] for b in read if nonzeroab(read[b])}
+    diff = len(read.keys()) - len(newread.keys())
+    if diff > 0:
+        sp.log(msg='{} bins have been discarded because no covered by any SNP\n'.format(diff), level="WARN")
+    return newread, samples
 
 
 def getPoints(data, samples):

src/hatchet/utils/combine_counts.py

@@ -44,6 +44,8 @@ def main(args=None):
 
     names = list(samples).sort()
     sys.stdout.write("#CHR\tSTART\tEND\tSAMPLE\tRD\t#SNPS\tCOV\tALPHA\tBETA\tBAF\n")
+    nonzerobaf = (lambda rk : all(sample[4] + sample[5] > 0 for sample in rk))
+    result = {key : result[key] for key in result if nonzerobaf(result[key])}
     for key in sorted(result, key=(lambda x : (sp.numericOrder(x[0]), int(x[1]), int(x[2])))):
         for sample in result[key]:
             sys.stdout.write("{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(key[0], key[1], key[2], sample[0], sample[1], sample[2], sample[3], sample[4], sample[5], sample[6]))