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Update CRAM detector output files. #8971

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Sep 4, 2024
Merged

Update CRAM detector output files. #8971

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16 changes: 8 additions & 8 deletions src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.tsv
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
file_name contig_name container_ordinal container_is_bad mismatch_rate alignment_start alignment_span
#No bad containers detected
#Good containers:
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 1 0 0.0066287128712871285 9999902 11055
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 2 0 0.0032158415841584157 10010859 11595
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 3 0 0.0028702970297029705 10022353 10302
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 4 0 0.0028138613861386137 10032556 10955
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 1 0 0.007091089108910891 9999901 5725
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 2 0 0.008675247524752475 10005525 4771
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 3 0 0.006677227722772277 10010195 6694
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 4 0 0.006946534653465347 10016789 6937
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 1 0 0.0066287128712871285 9999902 11055
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 2 0 0.0032158415841584157 10010859 11595
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 3 0 0.0028702970297029705 10022353 10302
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 4 0 0.0028138613861386137 10032556 10955
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 1 0 0.007091089108910891 9999901 5725
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 2 0 0.008675247524752475 10005525 4771
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 3 0 0.006677227722772277 10010195 6694
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 4 0 0.006946534653465347 10016789 6937
6 changes: 3 additions & 3 deletions src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
CRAM File Name: CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram
CRAM Version: 2.1
CRAM ID Contents: L1VzZXJzL2FraWV6dW4vSWRlYVA=
CRAM File Name: CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram
CRAM Version: 3.0
CRAM ID Contents: Li4vaHRzamRrL3NyYy90ZXN0L3I=

**********************NO CORRUPT CONTAINERS DETECTED**********************
Average mismatch rate for presumed good containers: 0.005615
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122 changes: 61 additions & 61 deletions src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.tsv
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,64 +1,64 @@
file_name contig_name container_ordinal container_is_bad mismatch_rate alignment_start alignment_span
#No bad containers detected
#Good containers:
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 1 0 0.0066287128712871285 9999902 11055
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 2 0 0.0032158415841584157 10010859 11595
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 3 0 0.0028702970297029705 10022353 10302
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 4 0 0.0028138613861386137 10032556 10955
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 5 0 0.0026405940594059407 10043410 11007
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 6 0 0.0023297029702970297 10054316 11415
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 7 0 0.004123762376237624 10065630 11707
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 8 0 0.0029712871287128715 10077236 10857
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 9 0 0.004207920792079208 10087992 12022
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 10 0 0.004023762376237624 10099914 11455
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 11 0 0.0033594059405940594 10111269 11677
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 12 0 0.0032445544554455447 10122847 11517
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 13 0 0.0025287128712871286 10134264 10812
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 14 0 0.0028118811881188118 10144976 11737
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 15 0 0.0027811881188118813 10156616 11103
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 16 0 0.003216831683168317 10167620 10903
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 17 0 0.0033316831683168316 10178422 10654
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 18 0 0.0028544554455445545 10188975 12280
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 19 0 0.002307920792079208 10201162 10498
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 20 0 0.0033574257425742575 10211560 11415
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 21 0 0.002822772277227723 10222875 10825
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 22 0 0.003494059405940594 10233602 11012
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 20 23 0 0.003443653463400968 10244514 5587
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 1 0 0.007091089108910891 9999901 5725
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 2 0 0.008675247524752475 10005525 4771
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 3 0 0.006677227722772277 10010195 6694
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 4 0 0.006946534653465347 10016789 6937
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 5 0 0.0074524752475247525 10023629 6933
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 6 0 0.009954455445544555 10030464 54819
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 7 0 0.027154455445544554 10085182 1209
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 8 0 0.010437623762376237 10086291 1849
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 9 0 0.007101980198019802 10088040 4846
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 10 0 0.0076544554455445545 10092786 5025
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 11 0 0.007856435643564356 10097710 4565
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 12 0 0.008387128712871287 10102174 5112
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 13 0 0.008465346534653466 10107185 4822
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 14 0 0.006217821782178218 10111906 4648
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 15 0 0.006370297029702971 10116453 5595
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 16 0 0.006818811881188119 10121948 4596
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 17 0 0.007886138613861386 10126444 4699
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 18 0 0.008905940594059405 10131043 4025
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 19 0 0.009242574257425742 10134967 3486
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 20 0 0.008777227722772278 10138352 2580
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 21 0 0.009877227722772277 10140831 2362
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 22 0 0.007791089108910891 10143092 3693
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 23 0 0.008422772277227722 10146684 3779
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 24 0 0.008382178217821782 10150362 3205
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 25 0 0.005921782178217822 10153467 4029
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 26 0 0.006862376237623763 10157395 3564
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 27 0 0.006395049504950495 10160858 3833
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 28 0 0.00555049504950495 10164591 4631
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 29 0 0.004498019801980198 10169122 5087
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 30 0 0.00440990099009901 10174110 5846
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 31 0 0.0058465346534653465 10179857 5196
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 32 0 0.005392079207920792 10184953 3979
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 33 0 0.005116831683168317 10188831 5765
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 34 0 0.005946534653465347 10194495 3216
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 35 0 0.0058 10197610 4759
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 36 0 0.00514950495049505 10202269 3867
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 37 0 0.004726732673267326 10206036 4706
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram 21 38 0 0.004119086417621911 10210641 5332
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 1 0 0.0066287128712871285 9999902 11055
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 2 0 0.0032158415841584157 10010859 11595
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 3 0 0.0028702970297029705 10022353 10302
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 4 0 0.0028138613861386137 10032556 10955
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 5 0 0.0026405940594059407 10043410 11007
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 6 0 0.0023297029702970297 10054316 11415
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 7 0 0.004123762376237624 10065630 11707
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 8 0 0.0029712871287128715 10077236 10857
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 9 0 0.004207920792079208 10087992 12022
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 10 0 0.004023762376237624 10099914 11455
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 11 0 0.0033594059405940594 10111269 11677
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 12 0 0.0032445544554455447 10122847 11517
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 13 0 0.0025287128712871286 10134264 10812
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 14 0 0.0028118811881188118 10144976 11737
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 15 0 0.0027811881188118813 10156616 11103
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 16 0 0.003216831683168317 10167620 10903
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 17 0 0.0033316831683168316 10178422 10654
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 18 0 0.0028544554455445545 10188975 12280
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 19 0 0.002307920792079208 10201162 10498
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 20 0 0.0033574257425742575 10211560 11415
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 21 0 0.002822772277227723 10222875 10825
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 22 0 0.003494059405940594 10233602 11012
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 20 23 0 0.003443653463400968 10244514 5587
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 1 0 0.007091089108910891 9999901 5725
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 2 0 0.008675247524752475 10005525 4771
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 3 0 0.006677227722772277 10010195 6694
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 4 0 0.006946534653465347 10016789 6937
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 5 0 0.0074524752475247525 10023629 6933
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 6 0 0.009954455445544555 10030464 54819
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 7 0 0.027154455445544554 10085182 1209
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 8 0 0.010437623762376237 10086291 1849
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 9 0 0.007101980198019802 10088040 4846
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 10 0 0.0076544554455445545 10092786 5025
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 11 0 0.007856435643564356 10097710 4565
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 12 0 0.008387128712871287 10102174 5112
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 13 0 0.008465346534653466 10107185 4822
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 14 0 0.006217821782178218 10111906 4648
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 15 0 0.006370297029702971 10116453 5595
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 16 0 0.006818811881188119 10121948 4596
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 17 0 0.007886138613861386 10126444 4699
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 18 0 0.008905940594059405 10131043 4025
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 19 0 0.009242574257425742 10134967 3486
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 20 0 0.008777227722772278 10138352 2580
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 21 0 0.009877227722772277 10140831 2362
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 22 0 0.007791089108910891 10143092 3693
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 23 0 0.008422772277227722 10146684 3779
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 24 0 0.008382178217821782 10150362 3205
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 25 0 0.005921782178217822 10153467 4029
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 26 0 0.006862376237623763 10157395 3564
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 27 0 0.006395049504950495 10160858 3833
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 28 0 0.00555049504950495 10164591 4631
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 29 0 0.004498019801980198 10169122 5087
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 30 0 0.00440990099009901 10174110 5846
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 31 0 0.0058465346534653465 10179857 5196
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 32 0 0.005392079207920792 10184953 3979
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 33 0 0.005116831683168317 10188831 5765
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 34 0 0.005946534653465347 10194495 3216
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 35 0 0.0058 10197610 4759
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 36 0 0.00514950495049505 10202269 3867
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 37 0 0.004726732673267326 10206036 4706
CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram 21 38 0 0.004119086417621911 10210641 5332
6 changes: 3 additions & 3 deletions src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
CRAM File Name: CEUTrio.HiSeq.WGS.b37.NA12878.20.21.cram
CRAM Version: 2.1
CRAM ID Contents: L1VzZXJzL2FraWV6dW4vSWRlYVA=
CRAM File Name: CEUTrio.HiSeq.WGS.b37.NA12878.20.21.v3.0.samtools.cram
CRAM Version: 3.0
CRAM ID Contents: Li4vaHRzamRrL3NyYy90ZXN0L3I=

**********************NO CORRUPT CONTAINERS DETECTED**********************
Average mismatch rate for presumed good containers: 0.005962
Expand Down
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