Re: [PATCH] Upgrade bedtools to 0.25.0.

2016-01-10 Thread Ben Woodcroft
On 10/01/16 06:32, Leo Famulari wrote: On Sat, Jan 09, 2016 at 07:07:42PM +0100, Ricardo Wurmus wrote: Ben Woodcroft writes: A reasonably straightforward update. I think you forgot to also remove the “bedtools-32bit-compilation.patch” file from “gnu/packages/patches”. In that case, the pa

Re: [PATCH] Upgrade bedtools to 0.25.0.

2016-01-09 Thread Leo Famulari
On Sat, Jan 09, 2016 at 07:07:42PM +0100, Ricardo Wurmus wrote: > > Ben Woodcroft writes: > > > A reasonably straightforward update. > > I think you forgot to also remove the “bedtools-32bit-compilation.patch” > file from “gnu/packages/patches”. In that case, the patch can also be "de-listed"

Re: [PATCH] Upgrade bedtools to 0.25.0.

2016-01-09 Thread Ricardo Wurmus
Ben Woodcroft writes: > A reasonably straightforward update. I think you forgot to also remove the “bedtools-32bit-compilation.patch” file from “gnu/packages/patches”. Otherwise I agree with Andreas about separating the stylistic from the functional changes by doing two commits. Thanks! ~~ R

Re: [PATCH] Upgrade bedtools to 0.25.0.

2016-01-09 Thread Ludovic Courtès
Andreas Enge skribis: > I do not have very strong feelings about the matter, but I do see the point > of separating stylistic and syntactic changes on one hand from functional > changes on the other hand. Then one can simply accept the former without > further checking; and the latter does not re

Re: [PATCH] Upgrade bedtools to 0.25.0.

2016-01-09 Thread Andreas Enge
On Sat, Jan 09, 2016 at 02:44:19PM +0100, Pjotr Prins wrote: > Sometimes I wonder if we are not being too prissy. Not exactly taxing > to read it in one commit and we can trust the committer to test it. I > see the point of agreed layouts and putting things in a *single* > commit. Now, for a change

Re: [PATCH] Upgrade bedtools to 0.25.0.

2016-01-09 Thread Pjotr Prins
On Sat, Jan 09, 2016 at 10:54:42AM +0100, Andreas Enge wrote: > On Sat, Jan 09, 2016 at 04:47:15PM +1000, Ben Woodcroft wrote: > > A reasonably straightforward update. > > If I remember correctly, it is common practice to do the move to modify-phases > and the update in two separate commits. Some

Re: [PATCH] Upgrade bedtools to 0.25.0.

2016-01-09 Thread Andreas Enge
On Sat, Jan 09, 2016 at 04:47:15PM +1000, Ben Woodcroft wrote: > A reasonably straightforward update. If I remember correctly, it is common practice to do the move to modify-phases and the update in two separate commits. Andreas

[PATCH] Upgrade bedtools to 0.25.0.

2016-01-08 Thread Ben Woodcroft
A reasonably straightforward update. Version 2.25.0 (3-Sept-2015) 1. Added new -F option that allows one to set the minimum fraction of overlap required for the B interval. This complements the functionality of the -f option.Available for intersect, coverage, map, subtract, and jaccard