quality padding is now set to Q40 for both possible offset values

frederic-mahe · frederic-mahe · commit be0bf9b48d78 · 2024-07-01T14:11:32.000+02:00
diff --git a/src/vsearch.cc b/src/vsearch.cc
@@ -5939,6 +5939,10 @@ auto main(int argc, char** argv) -> int
     }
   else if (parameters.opt_fastq_join)
     {
+      if ((not parameters.opt_join_padgapq_set_by_user) and
+          (parameters.opt_fastq_ascii != default_ascii_offset)) {
+        parameters.opt_join_padgapq = alternative_quality_padding;
+      }
       fastq_join(parameters);
     }
   else if (parameters.opt_rereplicate)

Original file line number	Diff line number	Diff line change
`@@ -5939,6 +5939,10 @@ auto main(int argc, char** argv) -> int`
`5939`	`5939`	`}`
`5940`	`5940`	`else if (parameters.opt_fastq_join)`
`5941`	`5941`	`{`
	`5942`	`+ if ((not parameters.opt_join_padgapq_set_by_user) and`
	`5943`	`+ (parameters.opt_fastq_ascii != default_ascii_offset)) {`
	`5944`	`+ parameters.opt_join_padgapq = alternative_quality_padding;`
	`5945`	`+ }`
`5942`	`5946`	`fastq_join(parameters);`
`5943`	`5947`	`}`
`5944`	`5948`	`else if (parameters.opt_rereplicate)`