Fix bug where empty chimeric read causes entire read remainder to be output

olliecheng · olliecheng · commit f35705f6b5ce · 2025-08-06T15:09:26.000+10:00
diff --git a/flexiplex.c++ b/flexiplex.c++
@@ -533,7 +533,7 @@ void print_read(string read_id, string read, string qual,
 
       for (int f = 0; f < vec_size; f++) {
         int temp_read_length = vec_bc.at(f).flank_start - read_start;
-        if (temp_read_length > 0 && temp_read_length < read_length)
+        if (temp_read_length >= 0 && temp_read_length < read_length)
           read_length = temp_read_length;
       }
       string qual_new = ""; // don't trim the quality scores if it's a fasta file
diff --git a/tests/output.fastq b/tests/output.fastq
@@ -14,9 +14,9 @@ DABC
 AAA
 +GGGG_#seq5_+2of2	CB:Z:GGGG	UB:Z:
 DAB
-@GGGG_#seq6_+1of1	CB:Z:GGGG	UB:Z:
+@GGGG_#seq6_+2of2	CB:Z:GGGG	UB:Z:
 C
-+GGGG_#seq6_+1of1	CB:Z:GGGG	UB:Z:
++GGGG_#seq6_+2of2	CB:Z:GGGG	UB:Z:
 =
 @GGGG_#seq7_+1of2	CB:Z:GGGG	UB:Z:
 A

Original file line number	Diff line number	Diff line change
`@@ -533,7 +533,7 @@ void print_read(string read_id, string read, string qual,`
`533`	`533`
`534`	`534`	`for (int f = 0; f < vec_size; f++) {`
`535`	`535`	`int temp_read_length = vec_bc.at(f).flank_start - read_start;`
`536`		`- if (temp_read_length > 0 && temp_read_length < read_length)`
	`536`	`+ if (temp_read_length >= 0 && temp_read_length < read_length)`
`537`	`537`	`read_length = temp_read_length;`
`538`	`538`	`}`
`539`	`539`	`string qual_new = ""; // don't trim the quality scores if it's a fasta file`