Mercurial > repos > iuc > varvamp

diff test-data/test3.log @ 2:baa1589657e1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp commit 7a60f4dbf7aecdc394570a48009e3283e4d83745
author iuc
date Thu, 05 Feb 2026 18:00:21 +0000
parents 7a586a157d37
children
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--- a/test-data/test3.log	Thu Feb 13 09:20:08 2025 +0000
+++ b/test-data/test3.log	Thu Feb 05 18:00:21 2026 +0000
@@ -1,4 +1,4 @@
-VARVAMP log 
+VARVAMP log
 
 MODE = qpcr
 
@@ -8,7 +8,7 @@
 THRESHOLD = 0.7
 PRIMER_ALLOWED_N_AMB = 1
 PROBE_ALLOWED_N_AMB = 1
-TEST_DELTAG_N_AMPLICONS = 180
+TEST_DELTAG_N_AMPLICONS = 10
 DELTAG_CUTOFF = -15
 
 CONFIG SETTINGS
@@ -20,7 +20,7 @@
 PRIMER_MAX_POLYX = 4
 PRIMER_MAX_DINUC_REPEATS = 4
 PRIMER_GC_END = (1, 3)
-PRIMER_MAX_DIMER_TMP = 47
+PRIMER_MAX_DIMER_TMP = 35
 PRIMER_MIN_3_WITHOUT_AMB = 3
 PCR_MV_CONC = 100
 PCR_DV_CONC = 2
@@ -32,6 +32,7 @@
 PRIMER_MAX_BASE_PENALTY = 10
 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
 PRIMER_PERMUTATION_PENALTY = 0.1
+END_OVERLAP = 5
 QPROBE_TMP = (64, 70, 67)
 QPROBE_SIZES = (20, 30, 25)
 QPROBE_GC_RANGE = (40, 80, 60)
@@ -42,4 +43,3 @@
 QAMPLICON_LENGTH = (70, 200)
 QAMPLICON_GC = (40, 60)
 QAMPLICON_DEL_CUTOFF = 4
-