[med-svn] [Git][med-team/gff2aplot][master] Replace tabs in gff files with spaces

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / gff2aplot


Commits:
ad844bca by Pranav Ballaney at 2020-06-14T11:55:03+05:30
Replace tabs in gff files with spaces

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/fix_gff_comments.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+gff2aplot (2.0-13) UNRELEASED; urgency=medium
+
+  * Replace tabs in gff files with spaces (Closes: #962553)
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com>  Sun, 14 Jun 2020 11:51:26 +0530
+
 gff2aplot (2.0-12) unstable; urgency=medium
 
   * Nelson A. de Oliveira retired from Debian (thanks for your previous


=====================================
debian/patches/fix_gff_comments.patch
=====================================
@@ -0,0 +1,33 @@
+Description: Replace tabs in gff files with spaces
+ GFFparsers are supposed to ignore all the text in lines that start with # but 
+ for some reason, gffread doesn't like tabs in comments.
+ The number of tabs after which gffread complains seems to be related to the 
+ following line, but since this is just a comment anyway, replacing tabs with
+ spaces seems like an easier fix.
+Author: Pranav Ballaney
+Bug-Debian: #962553
+Last-Update: 2020-06-14
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/examples/mhcregion/hs-mm.gff
++++ b/examples/mhcregion/hs-mm.gff
+@@ -3,7 +3,7 @@
+ ##date Jun/03/2003 15:19:51
+ ##
+ ##/home/ug/jabril/development/softjabril/gfftools/gff2aplot/bin/ali2gff  -x X87344 -y AF100956+AF027865 hs-mm.sim
+-#name1:name2		source		feature		beg1:beg2	end1:end2	score	strand	frame	group	comment
++#name1:name2               source      feature     beg1:beg2   end1:end2   score   strand frame group comment
+ X87344:AF100956+AF027865	sim96_LIN	seqbounds	1:1	32000:35000	.	.	.
+ X87344:AF100956+AF027865	sim96_LIN	alignment	863:804	19762:20115	18340.000	+:+	.:.
+ X87344:AF100956+AF027865	sim96_LIN	fragment	863:804	890:831	0.790	+:+	.:.	## cumulative nmp: 0.001
+--- a/examples/mhcregion/hs-mm.sim.gff
++++ b/examples/mhcregion/hs-mm.sim.gff
+@@ -3,7 +3,7 @@
+ ##date Jun/03/2003 16:41:22
+ ##
+ ## ali2gff  -x X87344 -y AF100956+AF027865 hs-mm.sim
+-#name1:name2		source		feature		beg1:beg2	end1:end2	score	strand	frame	group	comment
++#name1:name2               source      feature     beg1:beg2   end1:end2   score   strand  frame group comment
+ X87344:AF100956+AF027865	sim96_LIN	seqbounds	1:1	32000:35000	.	.	.
+ X87344:AF100956+AF027865	sim96_LIN	alignment	863:804	19762:20115	18340.000	+:+	.:.
+ X87344:AF100956+AF027865	sim96_LIN	fragment	863:804	890:831	0.790	+:+	.:.	## cumulative nmp: 0.001


=====================================
debian/patches/series
=====================================
@@ -8,3 +8,4 @@ perl_5.28.patch
 fix_install_ali2gff.patch
 enhance_sprintf_buffer.patch
 fix_README_used_for_test.patch
+fix_gff_comments.patch



View it on GitLab: https://salsa.debian.org/med-team/gff2aplot/-/commit/ad844bca4bb553cd49c1af15e6629360f508f50d

-- 
View it on GitLab: https://salsa.debian.org/med-team/gff2aplot/-/commit/ad844bca4bb553cd49c1af15e6629360f508f50d
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