From 87f1ddda36391b60414707db23413aba5801de5d Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@gmail.com>
Date: Fri, 13 Oct 2023 07:59:20 +0200
Subject: [PATCH] fix #383  (#402)

* sync doc

* fix #383 Can't continue outside a when block

---------

Co-authored-by: Jacques Dainat <jacques.dainat@ird.fr>
---
 bin/agat_convert_sp_gff2bed.pl        |  8 ++++----
 docs/tools/agat_convert_sp_gff2bed.md | 12 ++++++++++--
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/bin/agat_convert_sp_gff2bed.pl b/bin/agat_convert_sp_gff2bed.pl
index f189be6a..05ec8f88 100755
--- a/bin/agat_convert_sp_gff2bed.pl
+++ b/bin/agat_convert_sp_gff2bed.pl
@@ -190,11 +190,11 @@
 							$field12_blockStarts = undef;
 
 							if($test_nc eq "." and $opt_nc eq "filter"){
-								continue; # skip this non-coding feature
+								# skip this non-coding feature
+							} else {
+								# print bed line
+								print $bedout $line;
 							}
-							# print bed line
-							print $bedout $line;
-
 						}
 					}
 				}
diff --git a/docs/tools/agat_convert_sp_gff2bed.md b/docs/tools/agat_convert_sp_gff2bed.md
index bbe9e20e..a71cd62c 100644
--- a/docs/tools/agat_convert_sp_gff2bed.md
+++ b/docs/tools/agat_convert_sp_gff2bed.md
@@ -4,8 +4,9 @@
 
 The script aims to convert GTF/GXF file into bed file.
 It will convert level2 features from gff (mRNA, transcripts) into bed features.
-If  the selected level2 subfeatures (defaut: exon) exist, they will be reported
-in the block fields (9-12th colum in bed).
+If the selected level2 subfeatures (defaut: exon) exist, they are reported
+in the block fields (9-12th colum in bed). CDS Start and End are reported in column
+7 and 8 accordingly.
 
 Definintion of the bed format: 
 ```
@@ -37,6 +38,13 @@ agat_convert_sp_gff2bed.pl --help
 
     Input GFF3 file that will be read
 
+- **--nc**
+
+    STRING - behaviour for non-coding features (e.g. recored wihtout CDS). [keep,filter,transcript]
+    keep - Default, they are kept but no CDS position is reported in the 7th and 8th columns (a period is reported instead).
+    filter - We remove them.
+    transcript - We keep them but values in 7th and 8th columns will contains transcript's start and stop.
+
 - **--sub**
 
     Define the subfeature (level3, e.g exon,cds,utr,etc...) to report as blocks in the bed output.