e975034e529d38834c40b7c5b10519d2c06372f8
max
  Wed May 13 08:11:17 2020 -0700
making a few fixes to genbankToBigGenePred, refs #25114

diff --git src/utils/genbankToBigGenePred src/utils/genbankToBigGenePred
index 60d6279..fb0af70 100755
--- src/utils/genbankToBigGenePred
+++ src/utils/genbankToBigGenePred
@@ -123,47 +123,47 @@
         row.append(geneId)
         row.append("cmpl") # ???
         row.append("cmpl")
         row.append(exonFrames) # exonFrames
         row.append("N.a.") # transcript type
         row.append(geneId) # Primary identifier for gene
         row.append(geneId) # Alternative/human readable gene name
         row.append("N.a.") # Gene type
         row.append(ft.qualifiers.get("note", [""])[0]) # Notes
         row.append(protId) # Protein product ID
         row.append(xrefs.get("GeneID", "")) # NCBI Gene ID
         row.append(str(ft.extract(rec).seq)) # Gene type
         row.append("") # cDNA PSL
         row.append(repr(ft.qualifiers)) # protein sequence
         row.append("") # prot to cDNA PSL
-        row.append(repr(ft.qualifiers)) # anythign else
+        #row.append(repr(ft.qualifiers)) # anythign else
     else:
         row.append(ft.qualifiers.get("inference", [""])[0])
         row.append(ft.qualifiers.get("function", [""])[0])
         #row.append(repr(ft.qualifiers)) # anythign else, for debugging
 
     row = [str(x) for x in row]
     ofh.write("\t".join(row))
     ofh.write("\n")
 
 def bedToBigBed(fname, chromSizes, asName, bbDir):
     " convert bed to bigBed "
     cmd = ["bedSort", fname, fname]
     assert (subprocess.call(cmd)==0)
 
     outFname = basename(fname).replace(".bed", ".bb")
-    cmd = ["/cluster/home/braney/bin/x86_64/bedToBigBed", "-tab", "-type=bed12+", "-as="+asName, fname, chromSizes, join(bbDir, outFname)]
+    cmd = ["/cluster/home/braney/bin/x86_64/bedToBigBed", "-tab", "-type=bed12+", "-as="+asName, fname, chromSizes, join(bbDir, outFname), "-extraIndex=name", "-allow1bpOverlap"]
     logging.info("Running: "+(" ".join(cmd)))
     ret = subprocess.call(cmd)
     assert(ret==0)
 
 def gbToBigGenePred(fname, chromName, chromSizes, outDir, bbDir):
     outFnames = {
             "source" : join(outDir, "source.ra"),
             "genes" : join(outDir, "genes.bed"),
             "peptides" : join(outDir, "peptides.bed"),
             "other" : join(outDir, "other.bed"),
             }
 
     outFhs = {}
     for k, val in outFnames.items():
         outFhs[k] = open(val, "w")