[med-svn] [pbgenomicconsensus] 02/06: Align header lines on rst page to silence rst2man warnings

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
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commit c36c9acd6b138d4bbc0e4c38ef4250ab5383808f
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Mon Oct 12 22:50:24 2015 -0700

    Align header lines on rst page to silence rst2man warnings
---
 debian/patches/manpages.patch | 45 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/debian/patches/manpages.patch b/debian/patches/manpages.patch
index a075582..b2cb2c4 100644
--- a/debian/patches/manpages.patch
+++ b/debian/patches/manpages.patch
@@ -266,6 +266,51 @@ Last-Update: 2015-10-06
  What does Quiver put in its output files?
  -----------------------------------------
  There are three output files from Quiver:
+@@ -155,7 +159,7 @@
+ 
+ 
+ Does Quiver need to know what sequencing chemistry was used?
+-----------------------------------------------------------
++------------------------------------------------------------
+ 
+ At present, the Quiver model is trained per-chemistry, so it is very
+ important that Quiver knows the sequencing chemistries used.
+@@ -175,7 +179,7 @@
+ 
+ 
+ Can a mix of chemistries be used in a cmp.h5 file for Quiver?
+------------------------------------------------------------
++-------------------------------------------------------------
+ 
+ Yes!  Quiver automatically sees the chemistry *per-SMRT Cell*, so it
+ can figure out the right parameters for each read and model them
+@@ -289,7 +293,7 @@
+ 
+ 
+ How can the `MapQV` filter be turned off and when should it be?
+---------------------------------------------------------------
++---------------------------------------------------------------
+ The `MapQV` filter can be disabled using the flag
+ ``--mapQvThreshold=0`` (shorthand: ``-m=0``).  If running a
+ Quiver job via SMRT Portal, this can be done by unchecking the "Use
+@@ -299,7 +303,7 @@
+ 
+ 
+ How can variant calls made by Quiver be inspected or validated?
+---------------------------------------------------------------
++---------------------------------------------------------------
+ When in doubt, it is easiest to inspect the region in a tool like
+ SMRT View, which enables you to view the reads aligned to the region.
+ Deletions and substitutions should be fairly easy to spot; to view
+@@ -324,7 +328,7 @@
+ 
+ 
+ What happens when the sample is a mixture, or diploid?
+------------------------------------------------------
++------------------------------------------------------
+ At present, Quiver assumes a haploid sample, and the behavior of
+ *Quiver* on sample mixtures or diploid/polyploid samples is
+ *undefined*.  The program will not crash, but the output results are
 @@ -372,5 +376,10 @@
  calls.
  

-- 
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