Mercurial > repos > iuc > varvamp
annotate test-data/test4.log @ 4:36c91ff33d70 draft default tip
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86
author | iuc |
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date | Sat, 15 Jun 2024 15:43:28 +0000 |
parents | 462e62be07e1 |
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rev | line source |
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462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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1 VARVAMP log |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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2 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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3 MODE = single |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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4 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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5 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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6 ARG SETTINGS |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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7 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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8 THRESHOLD = 0.8 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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9 PRIMER_ALLOWED_N_AMB = 3 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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10 AMPLICON_OPT_LENGTH = 300 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
|
11 AMPLICON_MAX_LENGTH = 400 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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12 REPORT_N_AMPLICONS = 5 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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13 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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14 CONFIG SETTINGS |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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15 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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16 PRIMER_TMP = (56, 63, 60) |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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17 PRIMER_GC_RANGE = (20, 80, 50) |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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18 PRIMER_SIZES = (18, 24, 21) |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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19 PRIMER_HAIRPIN = 47 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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20 PRIMER_MAX_POLYX = 4 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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21 PRIMER_MAX_DINUC_REPEATS = 4 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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22 PRIMER_GC_END = (1, 3) |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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23 PRIMER_MAX_DIMER_TMP = 47 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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24 PRIMER_MIN_3_WITHOUT_AMB = 3 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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25 PCR_MV_CONC = 100.0 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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26 PCR_DV_CONC = 2.0 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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27 PCR_DNTP_CONC = 0.8 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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28 PCR_DNA_CONC = 15.0 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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29 PRIMER_TM_PENALTY = 2.0 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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30 PRIMER_GC_PENALTY = 0.2 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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31 PRIMER_SIZE_PENALTY = 0.5 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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32 PRIMER_MAX_BASE_PENALTY = 10 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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33 PRIMER_3_PENALTY = (32, 16, 8, 4, 2) |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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34 PRIMER_PERMUTATION_PENALTY = 0.1 |
462e62be07e1
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
iuc
parents:
diff
changeset
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35 |