Mercurial > repos > iuc > varvamp

diff test-data/test2.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 209d074eb024
children
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--- a/test-data/test2.log	Thu Feb 13 09:20:08 2025 +0000
+++ b/test-data/test2.log	Thu Feb 05 18:00:21 2026 +0000
@@ -1,9 +1,9 @@
-VARVAMP log 
+VARVAMP log
 
 MODE = tiled
 
 WARNING: your amplicon lengths might be to small. Consider increasing
-WARNING: your intended overlap is higher than half of your optimal length. This reduces how well varvamps will find overlapping amplicons. Consider decreasing.
+WARNING: your min overlap is lower than your optimal length / 2 - 2 * min primer length. This reduces how well varvamps will find overlapping amplicons. Consider decreasing.
 
 ARG SETTINGS
 
@@ -11,7 +11,7 @@
 PRIMER_ALLOWED_N_AMB = 2
 AMPLICON_OPT_LENGTH = 150
 AMPLICON_MAX_LENGTH = 300
-MIN_OVERLAP = 76
+MIN_OVERLAP = 40
 
 CONFIG SETTINGS
 
@@ -22,7 +22,7 @@
 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
@@ -34,4 +34,4 @@
 PRIMER_MAX_BASE_PENALTY = 10
 PRIMER_3_PENALTY = (32, 16, 8, 4, 2)
 PRIMER_PERMUTATION_PENALTY = 0.1
-
+END_OVERLAP = 5