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705 lines (678 loc) · 32.7 KB
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Testsuite: uk.ac.ebi.ena.sra.cram.TestAll
Tests run: 210, Failures: 2, Errors: 0, Time elapsed: 23.213 sec
------------- Standard Output ---------------
Expected: <3840>
got: <3839>
)
Expected: <6532>
got: <6531>
)
------------- ---------------- ---------------
------------- Standard Error -----------------
INFO CramWriter - Block purged: 1 10000 529 1255359 125.54 2.3247 0.718s 7410 16
INFO Bam2Cram - Codec stats:
Cram record codec 1248639 bits 10000 objects 124.86 bits/object
Heap bytes codec 281612 bits 89178 objects 3.16 bits/object
Mapping quality codec 10636 bits 9939 objects 1.07 bits/object
Rank codec 30197 bits 1287 objects 23.46 bits/object
Read flags codec 24338 bits 10000 objects 2.43 bits/object
Read name codec 754044 bits 7426 objects 101.54 bits/object
Record quality codec 10542 bits 6588 objects 1.60 bits/object
Refpos codec 10424 bits 10000 objects 1.04 bits/object
Variations codec 99587 bits 1634 objects 60.95 bits/object
Base QS codec 28105 bits 5579 objects 5.04 bits/object
Base change codec 4006 bits 2003 objects 2.00 bits/object
Base codec 15697 bits 6870 objects 2.28 bits/object
Deletion length codec 1 bits 1 objects 1.00 bits/object
Insert base codec 8438 bits 3576 objects 2.36 bits/object
Position in read 33757 bits 11159 objects 3.03 bits/object
Quality score codec 28105 bits 5579 objects 5.04 bits/object
Read feature operators 25280 bits 12793 objects 1.98 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 61
INFO Bam2Cram - Beyond horizon pairs: 7410, extra chromosomal pairs: 16
INFO Bam2Cram - Compressed bases: 540000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 545579
INFO Bam2Cram - Quality budget: 101.03%
INFO Bam2Cram - Total compression: 1.28
INFO Cram2Bam - CRAM format version: 0.9
INFO Cram2Bam - Using default quality score: ?
INFO Cram2Bam - Block read: sequence 1; records 10000; 0.190 seconds.
INFO Cram2Bam - Ref reading took 0 seconds.
INFO Cram2Bam - SAM/BAM writing took 0 seconds.
INFO Cram2Bam - Total time: 0 seconds.
INFO CramWriter - Block purged: 1 10000 529 1255359 125.54 2.3247 0.160s 7410 16
INFO Bam2Cram - Codec stats:
Cram record codec 1248639 bits 10000 objects 124.86 bits/object
Heap bytes codec 281612 bits 89178 objects 3.16 bits/object
Mapping quality codec 10636 bits 9939 objects 1.07 bits/object
Rank codec 30197 bits 1287 objects 23.46 bits/object
Read flags codec 24338 bits 10000 objects 2.43 bits/object
Read name codec 754044 bits 7426 objects 101.54 bits/object
Record quality codec 10542 bits 6588 objects 1.60 bits/object
Refpos codec 10424 bits 10000 objects 1.04 bits/object
Variations codec 99587 bits 1634 objects 60.95 bits/object
Base QS codec 28105 bits 5579 objects 5.04 bits/object
Base change codec 4006 bits 2003 objects 2.00 bits/object
Base codec 15697 bits 6870 objects 2.28 bits/object
Deletion length codec 1 bits 1 objects 1.00 bits/object
Insert base codec 8438 bits 3576 objects 2.36 bits/object
Position in read 33757 bits 11159 objects 3.03 bits/object
Quality score codec 28105 bits 5579 objects 5.04 bits/object
Read feature operators 25280 bits 12793 objects 1.98 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 61
INFO Bam2Cram - Beyond horizon pairs: 7410, extra chromosomal pairs: 16
INFO Bam2Cram - Compressed bases: 540000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 545579
INFO Bam2Cram - Quality budget: 101.03%
INFO Bam2Cram - Total compression: 1.28
INFO CramWriter - Block purged: 1 10000 941 5742406 574.24 10.6341 0.666s 7410 16
INFO Bam2Cram - Codec stats:
Cram record codec 5728230 bits 10000 objects 572.82 bits/object
Heap bytes codec 281612 bits 89178 objects 3.16 bits/object
Mapping quality codec 10636 bits 9939 objects 1.07 bits/object
Rank codec 30197 bits 1287 objects 23.46 bits/object
Read flags codec 24338 bits 10000 objects 2.43 bits/object
Read name codec 1010447 bits 10000 objects 101.04 bits/object
Record quality codec 1829413 bits 1080000 objects 1.69 bits/object
Refpos codec 10424 bits 10000 objects 1.04 bits/object
Tag key codec 401302 bits 109062 objects 3.68 bits/object
Variations codec 48782 bits 1634 objects 29.85 bits/object
Base change codec 4006 bits 2003 objects 2.00 bits/object
Base codec 16585 bits 6870 objects 2.41 bits/object
Deletion length codec 1 bits 1 objects 1.00 bits/object
Insert base codec 7892 bits 3576 objects 2.21 bits/object
Position in read 24396 bits 5580 objects 4.37 bits/object
Read feature operators 12487 bits 7214 objects 1.73 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 61
INFO Bam2Cram - Beyond horizon pairs: 7410, extra chromosomal pairs: 16
INFO Bam2Cram - Compressed bases: 540000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 540000
INFO Bam2Cram - Quality budget: 100.00%
INFO Bam2Cram - Total compression: 7.95
INFO Cram2Bam - CRAM format version: 0.9
INFO Cram2Bam - Using default quality score: ?
INFO Cram2Bam - Block read: sequence 1; records 10000; 0.266 seconds.
INFO Cram2Bam - Ref reading took 0 seconds.
INFO Cram2Bam - SAM/BAM writing took 0 seconds.
INFO Cram2Bam - Total time: 0 seconds.
INFO CramWriter - Block purged: 1 10000 988 5773641 577.36 10.6919 0.300s 7410 16
INFO Bam2Cram - Codec stats:
Cram record codec 5758777 bits 10000 objects 575.88 bits/object
Heap bytes codec 281612 bits 89178 objects 3.16 bits/object
Mapping quality codec 10636 bits 9939 objects 1.07 bits/object
Rank codec 30197 bits 1287 objects 23.46 bits/object
Read flags codec 24338 bits 10000 objects 2.43 bits/object
Read name codec 1010447 bits 10000 objects 101.04 bits/object
Record quality codec 1829413 bits 1080000 objects 1.69 bits/object
Refpos codec 10424 bits 10000 objects 1.04 bits/object
Tag key codec 416279 bits 111514 objects 3.73 bits/object
Variations codec 48782 bits 1634 objects 29.85 bits/object
Base change codec 4006 bits 2003 objects 2.00 bits/object
Base codec 16585 bits 6870 objects 2.41 bits/object
Deletion length codec 1 bits 1 objects 1.00 bits/object
Insert base codec 7892 bits 3576 objects 2.21 bits/object
Position in read 24396 bits 5580 objects 4.37 bits/object
Read feature operators 12487 bits 7214 objects 1.73 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 61
INFO Bam2Cram - Beyond horizon pairs: 7410, extra chromosomal pairs: 16
INFO Bam2Cram - Compressed bases: 540000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 540000
INFO Bam2Cram - Quality budget: 100.00%
INFO Bam2Cram - Total compression: 8.00
INFO CramWriter - Block purged: gi|66043271|ref|NC_007005.1| 10000 329 102479 10.25 0.2847 0.068s 0 0
INFO Bam2Cram - Codec stats:
Cram record codec 97991 bits 10000 objects 9.80 bits/object
Mapping quality codec 10000 bits 10000 objects 1.00 bits/object
Read flags codec 10000 bits 10000 objects 1.00 bits/object
Refpos codec 21994 bits 10000 objects 2.20 bits/object
Variations codec 35997 bits 1486 objects 24.22 bits/object
Base QS codec 7172 bits 1853 objects 3.87 bits/object
Base change codec 3704 bits 1852 objects 2.00 bits/object
Base codec 2 bits 1 objects 2.00 bits/object
Deletion length codec 8 bits 4 objects 2.00 bits/object
Insert base codec 2 bits 1 objects 2.00 bits/object
Position in read 15076 bits 3710 objects 4.06 bits/object
Quality score codec 7172 bits 1853 objects 3.87 bits/object
Read feature operators 10035 bits 5196 objects 1.93 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 0
INFO Bam2Cram - Beyond horizon pairs: 0, extra chromosomal pairs: 0
INFO Bam2Cram - Compressed bases: 360000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 361853
INFO Bam2Cram - Quality budget: 100.51%
INFO Bam2Cram - Total compression: 0.35
INFO Cram2Bam - CRAM format version: 0.9
INFO Cram2Bam - Using default quality score: ?
INFO Cram2Bam - Block read: sequence gi|66043271|ref|NC_007005.1|; records 10000; 0.091 seconds.
INFO Cram2Bam - Ref reading took 0 seconds.
INFO Cram2Bam - SAM/BAM writing took 0 seconds.
INFO Cram2Bam - Total time: 0 seconds.
INFO CramWriter - Block purged: gi|66043271|ref|NC_007005.1| 10000 329 102479 10.25 0.2847 0.041s 0 0
INFO Bam2Cram - Codec stats:
Cram record codec 97991 bits 10000 objects 9.80 bits/object
Mapping quality codec 10000 bits 10000 objects 1.00 bits/object
Read flags codec 10000 bits 10000 objects 1.00 bits/object
Refpos codec 21994 bits 10000 objects 2.20 bits/object
Variations codec 35997 bits 1486 objects 24.22 bits/object
Base QS codec 7172 bits 1853 objects 3.87 bits/object
Base change codec 3704 bits 1852 objects 2.00 bits/object
Base codec 2 bits 1 objects 2.00 bits/object
Deletion length codec 8 bits 4 objects 2.00 bits/object
Insert base codec 2 bits 1 objects 2.00 bits/object
Position in read 15076 bits 3710 objects 4.06 bits/object
Quality score codec 7172 bits 1853 objects 3.87 bits/object
Read feature operators 10035 bits 5196 objects 1.93 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 0
INFO Bam2Cram - Beyond horizon pairs: 0, extra chromosomal pairs: 0
INFO Bam2Cram - Compressed bases: 360000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 361853
INFO Bam2Cram - Quality budget: 100.51%
INFO Bam2Cram - Total compression: 0.35
INFO CramWriter - Block purged: gi|66043271|ref|NC_007005.1| 10000 545 1955095 195.51 5.4308 0.132s 0 0
INFO Bam2Cram - Codec stats:
Cram record codec 1947719 bits 10000 objects 194.77 bits/object
Mapping quality codec 10000 bits 10000 objects 1.00 bits/object
Read flags codec 10000 bits 10000 objects 1.00 bits/object
Read name codec 605057 bits 10000 objects 60.51 bits/object
Record quality codec 1060598 bits 720000 objects 1.47 bits/object
Refpos codec 21994 bits 10000 objects 2.20 bits/object
Tag key codec 160000 bits 60000 objects 2.67 bits/object
Variations codec 18581 bits 1486 objects 12.50 bits/object
Base change codec 3704 bits 1852 objects 2.00 bits/object
Base codec 2 bits 1 objects 2.00 bits/object
Deletion length codec 8 bits 4 objects 2.00 bits/object
Insert base codec 2 bits 1 objects 2.00 bits/object
Position in read 10028 bits 1857 objects 5.40 bits/object
Read feature operators 4839 bits 3343 objects 1.45 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 0
INFO Bam2Cram - Beyond horizon pairs: 0, extra chromosomal pairs: 0
INFO Bam2Cram - Compressed bases: 360000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 360000
INFO Bam2Cram - Quality budget: 100.00%
INFO Bam2Cram - Total compression: 4.51
INFO Cram2Bam - CRAM format version: 0.9
INFO Cram2Bam - Using default quality score: ?
INFO Cram2Bam - Block read: sequence gi|66043271|ref|NC_007005.1|; records 10000; 0.079 seconds.
INFO Cram2Bam - Ref reading took 0 seconds.
INFO Cram2Bam - SAM/BAM writing took 0 seconds.
INFO Cram2Bam - Total time: 0 seconds.
INFO CramWriter - Block purged: gi|66043271|ref|NC_007005.1| 10000 545 1955095 195.51 5.4308 0.137s 0 0
INFO Bam2Cram - Codec stats:
Cram record codec 1947719 bits 10000 objects 194.77 bits/object
Mapping quality codec 10000 bits 10000 objects 1.00 bits/object
Read flags codec 10000 bits 10000 objects 1.00 bits/object
Read name codec 605057 bits 10000 objects 60.51 bits/object
Record quality codec 1060598 bits 720000 objects 1.47 bits/object
Refpos codec 21994 bits 10000 objects 2.20 bits/object
Tag key codec 160000 bits 60000 objects 2.67 bits/object
Variations codec 18581 bits 1486 objects 12.50 bits/object
Base change codec 3704 bits 1852 objects 2.00 bits/object
Base codec 2 bits 1 objects 2.00 bits/object
Deletion length codec 8 bits 4 objects 2.00 bits/object
Insert base codec 2 bits 1 objects 2.00 bits/object
Position in read 10028 bits 1857 objects 5.40 bits/object
Read feature operators 4839 bits 3343 objects 1.45 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 0
INFO Bam2Cram - Beyond horizon pairs: 0, extra chromosomal pairs: 0
INFO Bam2Cram - Compressed bases: 360000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 360000
INFO Bam2Cram - Quality budget: 100.00%
INFO Bam2Cram - Total compression: 4.51
INFO CramWriter - Block purged: chrY 10000 458 493182 49.32 1.5412 0.081s 0 0
INFO Bam2Cram - Codec stats:
Cram record codec 487070 bits 10000 objects 48.71 bits/object
Mapping quality codec 34935 bits 10000 objects 3.49 bits/object
Read flags codec 10000 bits 10000 objects 1.00 bits/object
Refpos codec 91988 bits 10000 objects 9.20 bits/object
Variations codec 330147 bits 7781 objects 42.43 bits/object
Base QS codec 82841 bits 19496 objects 4.25 bits/object
Base change codec 38992 bits 19496 objects 2.00 bits/object
Position in read 134264 bits 38992 objects 3.44 bits/object
Quality score codec 82841 bits 19496 objects 4.25 bits/object
Read feature operators 74050 bits 46773 objects 1.58 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 0
INFO Bam2Cram - Beyond horizon pairs: 0, extra chromosomal pairs: 0
INFO Bam2Cram - Compressed bases: 320000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 339496
INFO Bam2Cram - Quality budget: 106.09%
INFO Bam2Cram - Total compression: 1.80
INFO Cram2Bam - CRAM format version: 0.9
INFO Cram2Bam - Using default quality score: ?
INFO Cram2Bam - Block read: sequence chrY; records 10000; 0.058 seconds.
INFO Cram2Bam - Ref reading took 0 seconds.
INFO Cram2Bam - SAM/BAM writing took 0 seconds.
INFO Cram2Bam - Total time: 0 seconds.
INFO CramWriter - Block purged: chrY 10000 458 493182 49.32 1.5412 0.070s 0 0
INFO Bam2Cram - Codec stats:
Cram record codec 487070 bits 10000 objects 48.71 bits/object
Mapping quality codec 34935 bits 10000 objects 3.49 bits/object
Read flags codec 10000 bits 10000 objects 1.00 bits/object
Refpos codec 91988 bits 10000 objects 9.20 bits/object
Variations codec 330147 bits 7781 objects 42.43 bits/object
Base QS codec 82841 bits 19496 objects 4.25 bits/object
Base change codec 38992 bits 19496 objects 2.00 bits/object
Position in read 134264 bits 38992 objects 3.44 bits/object
Quality score codec 82841 bits 19496 objects 4.25 bits/object
Read feature operators 74050 bits 46773 objects 1.58 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 0
INFO Bam2Cram - Beyond horizon pairs: 0, extra chromosomal pairs: 0
INFO Bam2Cram - Compressed bases: 320000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 339496
INFO Bam2Cram - Quality budget: 106.09%
INFO Bam2Cram - Total compression: 1.80
INFO CramWriter - Block purged: chrY 10000 686 2563850 256.39 8.0120 0.145s 0 0
INFO Bam2Cram - Codec stats:
Cram record codec 2554290 bits 10000 objects 255.43 bits/object
Mapping quality codec 34935 bits 10000 objects 3.49 bits/object
Read flags codec 10000 bits 10000 objects 1.00 bits/object
Read name codec 618530 bits 10000 objects 61.85 bits/object
Record quality codec 1400727 bits 640000 objects 2.19 bits/object
Refpos codec 91988 bits 10000 objects 9.20 bits/object
Tag key codec 80000 bits 40000 objects 2.00 bits/object
Variations codec 158154 bits 7781 objects 20.33 bits/object
Base change codec 38992 bits 19496 objects 2.00 bits/object
Position in read 91885 bits 19496 objects 4.71 bits/object
Read feature operators 27277 bits 27277 objects 1.00 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 0
INFO Bam2Cram - Beyond horizon pairs: 0, extra chromosomal pairs: 0
INFO Bam2Cram - Compressed bases: 320000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 320000
INFO Bam2Cram - Quality budget: 100.00%
INFO Bam2Cram - Total compression: 7.53
INFO Cram2Bam - CRAM format version: 0.9
INFO Cram2Bam - Using default quality score: ?
INFO Cram2Bam - Block read: sequence chrY; records 10000; 0.096 seconds.
INFO Cram2Bam - Ref reading took 0 seconds.
INFO Cram2Bam - SAM/BAM writing took 0 seconds.
INFO Cram2Bam - Total time: 0 seconds.
INFO CramWriter - Block purged: chrY 10000 686 2563850 256.39 8.0120 0.129s 0 0
INFO Bam2Cram - Codec stats:
Cram record codec 2554290 bits 10000 objects 255.43 bits/object
Mapping quality codec 34935 bits 10000 objects 3.49 bits/object
Read flags codec 10000 bits 10000 objects 1.00 bits/object
Read name codec 618530 bits 10000 objects 61.85 bits/object
Record quality codec 1400727 bits 640000 objects 2.19 bits/object
Refpos codec 91988 bits 10000 objects 9.20 bits/object
Tag key codec 80000 bits 40000 objects 2.00 bits/object
Variations codec 158154 bits 7781 objects 20.33 bits/object
Base change codec 38992 bits 19496 objects 2.00 bits/object
Position in read 91885 bits 19496 objects 4.71 bits/object
Read feature operators 27277 bits 27277 objects 1.00 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 0
INFO Bam2Cram - Beyond horizon pairs: 0, extra chromosomal pairs: 0
INFO Bam2Cram - Compressed bases: 320000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 320000
INFO Bam2Cram - Quality budget: 100.00%
INFO Bam2Cram - Total compression: 7.53
INFO CramWriter - Block purged: 1 10000 529 1255359 125.54 2.3247 0.114s 7410 16
INFO Bam2Cram - Codec stats:
Cram record codec 1248639 bits 10000 objects 124.86 bits/object
Heap bytes codec 281612 bits 89178 objects 3.16 bits/object
Mapping quality codec 10636 bits 9939 objects 1.07 bits/object
Rank codec 30197 bits 1287 objects 23.46 bits/object
Read flags codec 24338 bits 10000 objects 2.43 bits/object
Read name codec 754044 bits 7426 objects 101.54 bits/object
Record quality codec 10542 bits 6588 objects 1.60 bits/object
Refpos codec 10424 bits 10000 objects 1.04 bits/object
Variations codec 99587 bits 1634 objects 60.95 bits/object
Base QS codec 28105 bits 5579 objects 5.04 bits/object
Base change codec 4006 bits 2003 objects 2.00 bits/object
Base codec 15697 bits 6870 objects 2.28 bits/object
Deletion length codec 1 bits 1 objects 1.00 bits/object
Insert base codec 8438 bits 3576 objects 2.36 bits/object
Position in read 33757 bits 11159 objects 3.03 bits/object
Quality score codec 28105 bits 5579 objects 5.04 bits/object
Read feature operators 25280 bits 12793 objects 1.98 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 61
INFO Bam2Cram - Beyond horizon pairs: 7410, extra chromosomal pairs: 16
INFO Bam2Cram - Compressed bases: 540000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 545579
INFO Bam2Cram - Quality budget: 101.03%
INFO Bam2Cram - Total compression: 1.28
INFO Cram2Bam - CRAM format version: 0.9
INFO Cram2Bam - Using default quality score: ?
INFO Cram2Bam - Block read: sequence 1; records 10000; 0.060 seconds.
INFO Cram2Bam - Ref reading took 0 seconds.
INFO Cram2Bam - SAM/BAM writing took 0 seconds.
INFO Cram2Bam - Total time: 0 seconds.
INFO CramWriter - Block purged: 1 10000 529 1255359 125.54 2.3247 0.068s 7410 16
INFO Bam2Cram - Codec stats:
Cram record codec 1248639 bits 10000 objects 124.86 bits/object
Heap bytes codec 281612 bits 89178 objects 3.16 bits/object
Mapping quality codec 10636 bits 9939 objects 1.07 bits/object
Rank codec 30197 bits 1287 objects 23.46 bits/object
Read flags codec 24338 bits 10000 objects 2.43 bits/object
Read name codec 754044 bits 7426 objects 101.54 bits/object
Record quality codec 10542 bits 6588 objects 1.60 bits/object
Refpos codec 10424 bits 10000 objects 1.04 bits/object
Variations codec 99587 bits 1634 objects 60.95 bits/object
Base QS codec 28105 bits 5579 objects 5.04 bits/object
Base change codec 4006 bits 2003 objects 2.00 bits/object
Base codec 15697 bits 6870 objects 2.28 bits/object
Deletion length codec 1 bits 1 objects 1.00 bits/object
Insert base codec 8438 bits 3576 objects 2.36 bits/object
Position in read 33757 bits 11159 objects 3.03 bits/object
Quality score codec 28105 bits 5579 objects 5.04 bits/object
Read feature operators 25280 bits 12793 objects 1.98 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 61
INFO Bam2Cram - Beyond horizon pairs: 7410, extra chromosomal pairs: 16
INFO Bam2Cram - Compressed bases: 540000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 545579
INFO Bam2Cram - Quality budget: 101.03%
INFO Bam2Cram - Total compression: 1.28
INFO CramWriter - Block purged: 1 10000 941 5742406 574.24 10.6341 0.256s 7410 16
INFO Bam2Cram - Codec stats:
Cram record codec 5728230 bits 10000 objects 572.82 bits/object
Heap bytes codec 281612 bits 89178 objects 3.16 bits/object
Mapping quality codec 10636 bits 9939 objects 1.07 bits/object
Rank codec 30197 bits 1287 objects 23.46 bits/object
Read flags codec 24338 bits 10000 objects 2.43 bits/object
Read name codec 1010447 bits 10000 objects 101.04 bits/object
Record quality codec 1829413 bits 1080000 objects 1.69 bits/object
Refpos codec 10424 bits 10000 objects 1.04 bits/object
Tag key codec 401302 bits 109062 objects 3.68 bits/object
Variations codec 48782 bits 1634 objects 29.85 bits/object
Base change codec 4006 bits 2003 objects 2.00 bits/object
Base codec 16585 bits 6870 objects 2.41 bits/object
Deletion length codec 1 bits 1 objects 1.00 bits/object
Insert base codec 7892 bits 3576 objects 2.21 bits/object
Position in read 24396 bits 5580 objects 4.37 bits/object
Read feature operators 12487 bits 7214 objects 1.73 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 61
INFO Bam2Cram - Beyond horizon pairs: 7410, extra chromosomal pairs: 16
INFO Bam2Cram - Compressed bases: 540000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 540000
INFO Bam2Cram - Quality budget: 100.00%
INFO Bam2Cram - Total compression: 7.95
INFO Cram2Bam - CRAM format version: 0.9
INFO Cram2Bam - Using default quality score: ?
INFO Cram2Bam - Block read: sequence 1; records 10000; 0.212 seconds.
INFO Cram2Bam - Ref reading took 0 seconds.
INFO Cram2Bam - SAM/BAM writing took 0 seconds.
INFO Cram2Bam - Total time: 0 seconds.
INFO CramWriter - Block purged: 1 10000 988 5773641 577.36 10.6919 0.254s 7410 16
INFO Bam2Cram - Codec stats:
Cram record codec 5758777 bits 10000 objects 575.88 bits/object
Heap bytes codec 281612 bits 89178 objects 3.16 bits/object
Mapping quality codec 10636 bits 9939 objects 1.07 bits/object
Rank codec 30197 bits 1287 objects 23.46 bits/object
Read flags codec 24338 bits 10000 objects 2.43 bits/object
Read name codec 1010447 bits 10000 objects 101.04 bits/object
Record quality codec 1829413 bits 1080000 objects 1.69 bits/object
Refpos codec 10424 bits 10000 objects 1.04 bits/object
Tag key codec 416279 bits 111514 objects 3.73 bits/object
Variations codec 48782 bits 1634 objects 29.85 bits/object
Base change codec 4006 bits 2003 objects 2.00 bits/object
Base codec 16585 bits 6870 objects 2.41 bits/object
Deletion length codec 1 bits 1 objects 1.00 bits/object
Insert base codec 7892 bits 3576 objects 2.21 bits/object
Position in read 24396 bits 5580 objects 4.37 bits/object
Read feature operators 12487 bits 7214 objects 1.73 bits/object
INFO Bam2Cram - Found SAM records: 10000 unmapped: 61
INFO Bam2Cram - Beyond horizon pairs: 7410, extra chromosomal pairs: 16
INFO Bam2Cram - Compressed bases: 540000
INFO Bam2Cram - Landed ref masked qscores: 0
INFO Bam2Cram - Landed piled qscores: 0
INFO Bam2Cram - Landed total qscores: 540000
INFO Bam2Cram - Quality budget: 100.00%
INFO Bam2Cram - Total compression: 8.00
------------- ---------------- ---------------
Testcase: test1[0] took 1.855 sec
Testcase: test1[1] took 2.088 sec
Testcase: test1[2] took 0.427 sec
Testcase: test1[3] took 0.675 sec
Testcase: test1[4] took 0.604 sec
Testcase: test1[5] took 0.776 sec
Testcase: test1[6] took 0.495 sec
Testcase: test1[7] took 1.403 sec
Testcase: test_BaseChangeConstructorsWorkSimilar took 0.001 sec
Testcase: test_A_to_C_change took 0 sec
Testcase: test_all_possible_substituons took 0 sec
Testcase: test[0] took 0.001 sec
Testcase: test[1] took 0.001 sec
Testcase: test[2] took 0 sec
Testcase: test[3] took 0 sec
Testcase: test[4] took 0 sec
Testcase: test[5] took 0.001 sec
Testcase: test[6] took 0 sec
Testcase: test[7] took 0 sec
Testcase: test[8] took 0 sec
Testcase: test[9] took 0 sec
Testcase: test[10] took 0 sec
Testcase: test[11] took 0 sec
Testcase: test[12] took 0 sec
Testcase: test[13] took 0 sec
Testcase: test[14] took 0 sec
Testcase: test[15] took 0 sec
Testcase: test[16] took 0 sec
Testcase: test[17] took 0 sec
Testcase: test[18] took 0 sec
Testcase: test_ReadBits_8_bits took 0 sec
Testcase: test_ReadBits_3_bits_of_00000100 took 0 sec
Testcase: test_ReadBits_3_bits_of_01000000 took 0 sec
Testcase: test_ReadBits_31_bits_of_00000000000000000000000000000010 took 0 sec
Testcase: test_ReadBits_int_by_bit took 0.001 sec
Testcase: becnhmar_ReadBits_32 took 0.038 sec
Testcase: becnhmar_ReadLongBits_64 took 0.093 sec
Testcase: becnhmar_ReadLongBits_32 took 0.041 sec
Testcase: test_ReadBits_long_3_bits_of_01000000 took 0 sec
Testcase: test_ReadBits_int_range took 0.165 sec
Testcase: test_ReadBits_long_range took 0.173 sec
Testcase: test_write_long_64bits took 0.001 sec
Testcase: test_write_long_128_8_bits took 0 sec
Testcase: test_write_long_10bits took 0 sec
Testcase: test_write_long_2bits took 0 sec
Testcase: test_write_long_8bits took 0 sec
Testcase: benchmark_write_long took 0.071 sec
Testcase: test_write_int_32bits took 0 sec
Testcase: test_write_int_10bits took 0 sec
Testcase: test_write_int_2bits took 0 sec
Testcase: test_write_int_8bits took 0 sec
Testcase: benchmark_write_int took 0.031 sec
Testcase: test_write_byte_leftmost_bit took 0.001 sec
Testcase: test_WriteByte_all_possible_bytes took 0 sec
Testcase: test_write_long_higest_bit took 0 sec
Testcase: test_write_long_lowest_bit took 0 sec
Testcase: test_WriteBits_2_is_64_due_to_flush took 0 sec
Testcase: test_Write_int_32_bits took 0.001 sec
Testcase: benchmark_Write_int_32_bits took 0.032 sec
Testcase: test_3_bits_of_byte took 0 sec
Testcase: test_all_possible_bytes took 0.001 sec
Testcase: test_bits_1_to_8 took 0 sec
Testcase: testWrite_read_int_by_bit took 0 sec
Testcase: testWrite_read_32_bits took 0 sec
Testcase: testWrite_MaxInteger took 0 sec
Testcase: testWrite_MinInteger took 0 sec
Testcase: testWriteReadBenchmark took 0.092 sec
Testcase: testWriteReadLongBenchmark took 0.107 sec
Testcase: test_Align took 0.011 sec
Testcase: test1[0] took 0.002 sec
Testcase: test1[1] took 0.002 sec
Testcase: testEmptyLine took 0.002 sec
Testcase: failEmptyLineWithSlashN took 0 sec
Testcase: test_1 took 0 sec
Testcase: fail_1n took 0 sec
Testcase: test_xyxxyyx took 0 sec
Testcase: test_numberOfBits took 0 sec
Testcase: test_write_read_1 took 0 sec
Testcase: test_write_read_2 took 0 sec
Testcase: test_write_read_20 took 0.001 sec
Testcase: test_write_read_128 took 0 sec
Testcase: test_write_read_1_to_1000_offset_0 took 0.002 sec
Testcase: test_write_read_0_to_1000_offset_1 took 0.003 sec
Testcase: benchmark_write_read took 0.183 sec
Testcase: test_numberOfBits took 0 sec
Testcase: test_write_read_1 took 0 sec
Testcase: test_write_14_3 took 0 sec
Testcase: test_read_14_3 took 0 sec
Testcase: test_write_14_4 took 0 sec
Testcase: test_read_14_43 took 0 sec
Testcase: test_1 took 0 sec
Testcase: test_numberOfBits took 0 sec
Testcase: test_0 took 0 sec
Testcase: test_20 took 0.001 sec
Testcase: test_255 took 0 sec
Testcase: benchmark_uniform_distr took 2.084 sec
Testcase: benchmark_exponential_distr took 2.677 sec
Testcase: benchmark_normal_distr took 6.17 sec
Testcase: becnmark_Write took 0.103 sec
Testcase: becnmark_Read took 0.043 sec
Testcase: test_write_1 took 0 sec
Testcase: test_write_2 took 0 sec
Testcase: test_write_1_2_3_4 took 0 sec
Testcase: test_write_read_random took 0.007 sec
Testcase: benchmark_write_read_random took 0.149 sec
Testcase: benchmark_read_random took 0.007 sec
Testcase: test_write_1 took 0.001 sec
Testcase: test_write_2 took 0 sec
Testcase: test_write_1_2_3_4 took 0 sec
Testcase: test_write_read_random took 0.003 sec
Testcase: benchmark_write_read_random took 0.117 sec
Testcase: test_write_1 took 0 sec
Testcase: test_write_2 took 0 sec
Testcase: test_write_1_2_3_4 took 0 sec
Testcase: test_write_read_random took 0.001 sec
Testcase: benchmark_write_read_random took 0.128 sec
Testcase: test1 took 0.002 sec
Testcase: test2 took 0.001 sec
Testcase: test3 took 0.001 sec
Testcase: test4 took 0 sec
Testcase: test5 took 0.003 sec
FAILED
Expected: <3840>
got: <3839>
junit.framework.AssertionFailedError:
Expected: <3840>
got: <3839>
Expected: <3840>
got: <3839>
at uk.ac.ebi.ena.sra.cram.bam.InsertSizeTest.assertInsertSize(InsertSizeTest.java:60)
at uk.ac.ebi.ena.sra.cram.bam.InsertSizeTest.test5(InsertSizeTest.java:196)
Testcase: test6 took 0.001 sec
FAILED
Expected: <6532>
got: <6531>
junit.framework.AssertionFailedError:
Expected: <6532>
got: <6531>
Expected: <6532>
got: <6531>
at uk.ac.ebi.ena.sra.cram.bam.InsertSizeTest.assertInsertSize(InsertSizeTest.java:60)
at uk.ac.ebi.ena.sra.cram.bam.InsertSizeTest.test6(InsertSizeTest.java:225)
Testcase: testEmptyLine took 0 sec
Testcase: failEmptyLineWithSlashN took 0 sec
Testcase: test_1 took 0 sec
Testcase: fail_1n took 0 sec
Testcase: fail_non_digit took 0 sec
Testcase: test_1_2 took 0 sec
Testcase: test_1_3_15 took 0 sec
Testcase: test_ReadBits_8_bits took 0.001 sec
Testcase: test_ReadBits_3_bits_of_00000100 took 0 sec
Testcase: test_ReadBits_3_bits_of_01000000 took 0 sec
Testcase: test_ReadBits_31_bits_of_00000000000000000000000000000010 took 0 sec
Testcase: test_ReadBits_int_by_bit took 0 sec
Testcase: becnhmar_ReadBits_32 took 0.05 sec
Testcase: becnhmar_ReadLongBits_64 took 0.399 sec
Testcase: becnhmar_ReadLongBits_32 took 0.199 sec
Testcase: test_ReadBits_long_3_bits_of_01000000 took 0 sec
Testcase: test_ReadBits_int_range took 0.182 sec
Testcase: test_ReadBits_long_range took 0.302 sec
Testcase: test_3_bits_of_byte took 0 sec
Testcase: test_all_possible_bytes took 0 sec
Testcase: test_bits_1_to_8 took 0 sec
Testcase: testWrite_read_int_by_bit took 0.001 sec
Testcase: testWrite_read_32_bits took 0 sec
Testcase: testWrite_MaxInteger took 0 sec
Testcase: testWrite_MinInteger took 0 sec
Testcase: testWriteReadBenchmark took 0.104 sec
Testcase: test_all_encodings_have_codec took 0.001 sec
Testcase: test_string_representation_round_trip took 0 sec
Testcase: test1 took 0.001 sec
Testcase: test[0] took 0 sec
Testcase: test[1] took 0 sec
Testcase: test[2] took 0 sec
Testcase: test[3] took 0 sec
Testcase: test[4] took 0 sec
Testcase: test[5] took 0 sec
Testcase: test[6] took 0 sec
Testcase: test[7] took 0 sec
Testcase: test[8] took 0 sec
Testcase: test[9] took 0 sec
Testcase: test[10] took 0 sec
Testcase: test1 took 0 sec
Testcase: test2 took 0 sec
Testcase: test3 took 0 sec
Testcase: test4 took 0.001 sec
Testcase: test5 took 0 sec
Testcase: test6 took 0 sec
Testcase: test7 took 0 sec
Testcase: test8 took 0 sec
Testcase: test9 took 0 sec
Testcase: test10 took 0.001 sec
Testcase: test1 took 0 sec
Testcase: test2 took 0.001 sec
Testcase: test3 took 0 sec
Testcase: test4 took 0 sec
Testcase: test5 took 0.001 sec
Testcase: test6 took 0 sec
Testcase: test_Reversed_read took 0 sec
Testcase: testIntegerListMaskFactory took 0 sec
Testcase: testFastaByteArrayMaskFactory took 0 sec
Testcase: test_numberOfBits took 0 sec
Testcase: test_write_14_3 took 0.001 sec
Testcase: test_read_14_3 took 0 sec
Testcase: test_write_14_4 took 0 sec
Testcase: test_write_0_3 took 0 sec
Testcase: test_write_1_3 took 0 sec
Testcase: test_read_14_4 took 0 sec
Testcase: test1 took 0 sec
Testcase: test1[0] took 0.002 sec
Testcase: test1 took 0.005 sec
Testcase: test2 took 0.006 sec
Testcase: test3 took 0.006 sec
Testcase: test4 took 0.006 sec
Testcase: testSourceSize took 0 sec
Testcase: testRestoredSize took 0 sec
Testcase: testBases took 0.001 sec
Testcase: testQualityScores took 0.001 sec
Testcase: testFlags took 0 sec
Testcase: testAlignmentStart took 0 sec
Testcase: testReferenceName took 0 sec
Testcase: testMateReferenceName took 0 sec
Testcase: testMateAlignmentStart took 0 sec
Testcase: testMateNegativeStrandFlag took 0 sec
Testcase: testMateUnmappedFlag took 0 sec
Testcase: test_numberOfBits took 0.001 sec
Testcase: test_write_read_20 took 0 sec
Testcase: benchmark_write_read took 0.291 sec
Testcase: test_write_read_0 took 0 sec
Testcase: test_write_read_0_to_1000 took 0.557 sec