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biopet.biopet
Commits
c16a5040
Commit
c16a5040
authored
Oct 05, 2014
by
bow
Browse files
Update WipeReads test cases
parent
457d3655
Changes
4
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biopet-framework/src/test/resources/paired01.bam
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c16a5040
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biopet-framework/src/test/resources/paired01.bam.bai
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biopet-framework/src/test/resources/paired01.sam
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c16a5040
...
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@@ -11,7 +11,7 @@ r04 99 chrQ 450 60 10M = 490 50 CGTACGTACG EEFFGGHHII RG:Z:001
r04 147 chrQ 490 60 10M = 450 -50 GCATGCATGC EEFFGGHHII RG:Z:001
r03 163 chrQ 650 60 10M = 690 50 TTTTTCCCCC HHHHHHHHHH RG:Z:001
r03 83 chrQ 690 60 10M = 650 -50 CCCCCTTTTT HHHHHHHHHH RG:Z:001
r05 99 chrQ 8
5
0 60 5M
1
00N5M = 1
29
0 50 TACGTACGTA EEFFGGHHII RG:Z:001
r05 147 chrQ 1
29
0 60
5M100N5
M =
125
0 -50 ATGCATGCAT EEFFGGHHII RG:Z:001
r05 99 chrQ 8
9
0 60 5M
2
00N5M = 1
14
0 50 TACGTACGTA EEFFGGHHII RG:Z:001
r05 147 chrQ 1
14
0 60
10
M =
89
0 -50 ATGCATGCAT EEFFGGHHII RG:Z:001
r06 4 * 0 0 * * 0 0 ATATATATAT HIHIHIHIHI RG:Z:001
r06 4 * 0 0 * * 0 0 GCGCGCGCGC HIHIHIHIHI RG:Z:001
biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/apps/WipeReadsUnitTest.scala
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c16a5040
...
...
@@ -171,8 +171,8 @@ class WipeReadsUnitTest extends Assertions {
assert
(
isFilteredOut
(
"r04\t99\tchrQ\t450\t60\t10M\t=\t490\t50\tCGTACGTACG\tEEFFGGHHII\tRG:Z:001\n"
))
assert
(
isFilteredOut
(
"r04\t147\tchrQ\t490\t60\t10M\t=\t450\t-50\tGCATGCATGC\tEEFFGGHHII\tRG:Z:001\n"
))
/* TODO: exclude r05 from set
assert(!isFilteredOut("r05\t99\tchrQ\t850\t60\t5M100N5M\t=\t1
29
0\t50\tTACGTACGTA\tEEFFGGHHII\tRG:Z:001\n"))
assert(!isFilteredOut("r05\t147\tchrQ\t1
29
0\t60\t
5M100N5
M\t=\t
12
50\t-50\tATGCATGCAT\tEEFFGGHHII\tRG:Z:001\n"))
assert(!isFilteredOut("r05\t99\tchrQ\t850\t60\t5M100N5M\t=\t1
14
0\t50\tTACGTACGTA\tEEFFGGHHII\tRG:Z:001\n"))
assert(!isFilteredOut("r05\t147\tchrQ\t1
14
0\t60\t
10
M\t=\t
8
50\t-50\tATGCATGCAT\tEEFFGGHHII\tRG:Z:001\n"))
*/
}
...
...
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