Mercurial > repos > iuc > varvamp

comparison test-data/test4.log @ 0:462e62be07e1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
author iuc
date Sat, 27 Jan 2024 12:34:39 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:462e62be07e1
1 VARVAMP log
2
3 MODE = single
4
5
6 ARG SETTINGS
7
8 THRESHOLD = 0.8
9 PRIMER_ALLOWED_N_AMB = 3
10 AMPLICON_OPT_LENGTH = 300
11 AMPLICON_MAX_LENGTH = 400
12 REPORT_N_AMPLICONS = 5
13
14 CONFIG SETTINGS
15
16 PRIMER_TMP = (56, 63, 60)
17 PRIMER_GC_RANGE = (20, 80, 50)
18 PRIMER_SIZES = (18, 24, 21)
19 PRIMER_HAIRPIN = 47
20 PRIMER_MAX_POLYX = 4
21 PRIMER_MAX_DINUC_REPEATS = 4
22 PRIMER_GC_END = (1, 3)
23 PRIMER_MAX_DIMER_TMP = 47
24 PRIMER_MIN_3_WITHOUT_AMB = 3
25 PCR_MV_CONC = 100.0
26 PCR_DV_CONC = 2.0
27 PCR_DNTP_CONC = 0.8
28 PCR_DNA_CONC = 15.0
29 PRIMER_TM_PENALTY = 2.0
30 PRIMER_GC_PENALTY = 0.2
31 PRIMER_SIZE_PENALTY = 0.5
32 PRIMER_MAX_BASE_PENALTY = 10
33 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
34 PRIMER_PERMUTATION_PENALTY = 0.1
35