diff --git a/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.tsv b/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.tsv index 5155b23ec65..736055fa5e3 100644 --- a/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.tsv +++ b/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.tsv @@ -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 diff --git a/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.txt b/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.txt index 0c9b47663d6..d87b415b46d 100644 --- a/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.txt +++ b/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.false.bug8768.txt @@ -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 diff --git a/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.tsv b/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.tsv index ac064bf09bf..fb7c955276c 100644 --- a/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.tsv +++ b/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.tsv @@ -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 diff --git a/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.txt b/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.txt index 29f906bc803..0f6adc139ed 100644 --- a/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.txt +++ b/src/test/resources/filediagnostics/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.true.bug8768.txt @@ -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