shorten mutid

bin/addsv.py

@@ -324,7 +324,8 @@ def makemut(args, bedline, alignopts):
 
     if args.seed is not None: random.seed(int(args.seed) + int(bedline.strip().split()[1]))
 
-    mutid = '_'.join(map(str, bedline.strip().split()))
+    mutid = '_'.join(map(str, bedline.strip().split()[:4]))
+
     try:
         bamfile = pysam.Samfile(args.bamFileName, 'rb')
         reffile = pysam.Fastafile(args.refFasta)

scripts/postprocess.py

@@ -125,15 +125,15 @@ def makebam(sam, fai, threads, mem):
     cmd = ['samtools', 'view', '-bt', fai, '-o', outbam, sam]
     sys.stderr.write(sam + ' --> ' + outbam + ': ' + ' '.join(cmd) + '\n')
     call(cmd)
-    remove(sam)
+    #remove(sam)
 
     outsort = sub('.bam$', '.sorted.bam', outbam)
     cmd = ['samtools', 'sort', '-m', str(mem), '-@', str(threads), '-T', outsort, '-o',  outsort, outbam]
     outsort += '.bam'
     sys.stderr.write(outbam + ' --> ' + outsort + ': ' + ' '.join(cmd) + '\n')
     call(cmd)
 
-    remove(outbam)
+    #remove(outbam)
 
 
 def main(args):

scripts/remove_unpaired.py

@@ -15,16 +15,17 @@
     reads = {}
 
     for read in inbam.fetch(until_eof=True):
-        if read.qname in reads:
-            reads[read.qname].append(read)
-        else:
-            reads[read.qname] = []
-            reads[read.qname].append(read)
-
-        if len(reads[read.qname]) == 2:
-            for outread in reads[read.qname]:
-                outbam.write(outread)
-            del reads[read.qname]
+        if not read.is_secondary and not read.is_supplementary:
+            if read.qname in reads:
+                reads[read.qname].append(read)
+            else:
+                reads[read.qname] = []
+                reads[read.qname].append(read)
+
+            if len(reads[read.qname]) == 2:
+                for outread in reads[read.qname]:
+                    outbam.write(outread)
+                del reads[read.qname]
 
     inbam.close()
     outbam.close()

test/test_snv.sh

@@ -41,7 +41,7 @@ then
     exit 65
 fi
 
-addsnv.py -v ../test_data/random_snvs.txt -f ../test_data/testregion_realign.bam -r $3 -o ../test_data/testregion_mut.bam -n $1 -p $2 --ignoresnps --ignorepileup --seed 1234
+addsnv.py -z 100 -v ../test_data/random_snvs.txt -f ../test_data/testregion_realign.bam -r $3 -o ../test_data/testregion_mut.bam -n $1 -p $2 --ignoresnps --ignorepileup --seed 1234
 if [ $? -ne 0 ]
 then
  echo "addsnv.py failed. Are all the prequisites installed?"

test_data/random_snvs.txt

@@ -1,4 +1,5 @@
-22	34166720	34166721 1.0
+22	34166720	34166720 1.0
+22	34166721	34166721 1.0
 22	33908770	33908771 0.15
 22	33714964	33714965 0.5
 22	33769483	33769484 0.75