From 2428d35a463ab88ac060ad89d5bec5eaf922646b Mon Sep 17 00:00:00 2001
From: jayhesselberth <jay.hesselberth@gmail.com>
Date: Sat, 8 Feb 2014 13:01:45 -0700
Subject: [PATCH] * modified rst to add labels for inclusion in objects.inv &
 intersphinx * capability

---
 docs/content/tools/annotate.rst    | 2 ++
 docs/content/tools/bamtobed.rst    | 2 ++
 docs/content/tools/bamtofastq.rst  | 2 ++
 docs/content/tools/bed12tobed6.rst | 2 ++
 docs/content/tools/bedpetobam.rst  | 4 +++-
 docs/content/tools/bedtobam.rst    | 2 ++
 docs/content/tools/closest.rst     | 2 ++
 docs/content/tools/cluster.rst     | 2 ++
 docs/content/tools/complement.rst  | 2 ++
 docs/content/tools/coverage.rst    | 2 ++
 docs/content/tools/expand.rst      | 4 +++-
 docs/content/tools/flank.rst       | 2 ++
 docs/content/tools/genomecov.rst   | 2 ++
 docs/content/tools/getfasta.rst    | 2 ++
 docs/content/tools/groupby.rst     | 2 ++
 docs/content/tools/igv.rst         | 4 +++-
 docs/content/tools/intersect.rst   | 2 ++
 docs/content/tools/jaccard.rst     | 2 ++
 docs/content/tools/links.rst       | 2 ++
 docs/content/tools/makewindows.rst | 4 +++-
 docs/content/tools/map.rst         | 2 ++
 docs/content/tools/maskfasta.rst   | 2 ++
 docs/content/tools/merge.rst       | 2 ++
 docs/content/tools/multicov.rst    | 4 +++-
 docs/content/tools/multiinter.rst  | 4 +++-
 docs/content/tools/nuc.rst         | 4 +++-
 docs/content/tools/overlap.rst     | 2 ++
 docs/content/tools/pairtobed.rst   | 4 +++-
 docs/content/tools/pairtopair.rst  | 4 +++-
 docs/content/tools/random.rst      | 2 ++
 docs/content/tools/reldist.rst     | 2 ++
 docs/content/tools/shuffle.rst     | 2 ++
 docs/content/tools/slop.rst        | 2 ++
 docs/content/tools/sort.rst        | 2 ++
 docs/content/tools/subtract.rst    | 2 ++
 docs/content/tools/tag.rst         | 4 +++-
 docs/content/tools/unionbedg.rst   | 4 +++-
 docs/content/tools/window.rst      | 2 ++
 38 files changed, 87 insertions(+), 11 deletions(-)

diff --git a/docs/content/tools/annotate.rst b/docs/content/tools/annotate.rst
index eb0a4aa4..3345a7dc 100755
--- a/docs/content/tools/annotate.rst
+++ b/docs/content/tools/annotate.rst
@@ -1,3 +1,5 @@
+.. _annotate:
+
 ###############
 *annotate*
 ###############
diff --git a/docs/content/tools/bamtobed.rst b/docs/content/tools/bamtobed.rst
index 2096cf52..2cb22f86 100755
--- a/docs/content/tools/bamtobed.rst
+++ b/docs/content/tools/bamtobed.rst
@@ -1,3 +1,5 @@
+.. _bamtobed:
+
 ###############
 *bamtobed*
 ###############
diff --git a/docs/content/tools/bamtofastq.rst b/docs/content/tools/bamtofastq.rst
index 3757991d..217d678f 100644
--- a/docs/content/tools/bamtofastq.rst
+++ b/docs/content/tools/bamtofastq.rst
@@ -1,3 +1,5 @@
+.. _bamtofastq:
+
 ###############
 *bamtofastq*
 ###############
diff --git a/docs/content/tools/bed12tobed6.rst b/docs/content/tools/bed12tobed6.rst
index 9b41e5c9..e29105b5 100755
--- a/docs/content/tools/bed12tobed6.rst
+++ b/docs/content/tools/bed12tobed6.rst
@@ -1,3 +1,5 @@
+.. _bed12tobed6:
+
 ###############
 *bed12tobed6*
 ###############
diff --git a/docs/content/tools/bedpetobam.rst b/docs/content/tools/bedpetobam.rst
index d40e1a7d..92151b63 100644
--- a/docs/content/tools/bedpetobam.rst
+++ b/docs/content/tools/bedpetobam.rst
@@ -1,3 +1,5 @@
+.. _bedpetobam:
+
 ###############
 *bedpetobam*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/bedtobam.rst b/docs/content/tools/bedtobam.rst
index 6e1183af..3177dd0c 100755
--- a/docs/content/tools/bedtobam.rst
+++ b/docs/content/tools/bedtobam.rst
@@ -1,3 +1,5 @@
+.. _bedtobam:
+
 ###############
 *bedtobam*
 ###############
diff --git a/docs/content/tools/closest.rst b/docs/content/tools/closest.rst
index f0449567..aa137566 100755
--- a/docs/content/tools/closest.rst
+++ b/docs/content/tools/closest.rst
@@ -1,3 +1,5 @@
+.. _closest:
+
 ###############
 *closest*
 ###############
diff --git a/docs/content/tools/cluster.rst b/docs/content/tools/cluster.rst
index 9f4f6f37..90a5c8b9 100644
--- a/docs/content/tools/cluster.rst
+++ b/docs/content/tools/cluster.rst
@@ -1,3 +1,5 @@
+.. _cluster:
+
 ###############
 *cluster*
 ###############
diff --git a/docs/content/tools/complement.rst b/docs/content/tools/complement.rst
index 05d4abaf..a3c850f9 100755
--- a/docs/content/tools/complement.rst
+++ b/docs/content/tools/complement.rst
@@ -1,3 +1,5 @@
+.. _complement:
+
 ###############
 *complement*
 ###############
diff --git a/docs/content/tools/coverage.rst b/docs/content/tools/coverage.rst
index 9d884a43..f5de907c 100755
--- a/docs/content/tools/coverage.rst
+++ b/docs/content/tools/coverage.rst
@@ -1,3 +1,5 @@
+.. _coverage:
+
 ###############
 *coverage*
 ###############
diff --git a/docs/content/tools/expand.rst b/docs/content/tools/expand.rst
index 5b0126f4..15b53f65 100644
--- a/docs/content/tools/expand.rst
+++ b/docs/content/tools/expand.rst
@@ -1,3 +1,5 @@
+.. _expand:
+
 ###############
 *expand*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/flank.rst b/docs/content/tools/flank.rst
index a210ef69..db3b9da4 100644
--- a/docs/content/tools/flank.rst
+++ b/docs/content/tools/flank.rst
@@ -1,3 +1,5 @@
+.. _flank:
+
 ###############
 *flank*
 ###############
diff --git a/docs/content/tools/genomecov.rst b/docs/content/tools/genomecov.rst
index e0c73a6e..e5fd0553 100755
--- a/docs/content/tools/genomecov.rst
+++ b/docs/content/tools/genomecov.rst
@@ -1,3 +1,5 @@
+.. _genomecov:
+
 ###############
 *genomecov*
 ###############
diff --git a/docs/content/tools/getfasta.rst b/docs/content/tools/getfasta.rst
index d9ff1046..7c65ceb0 100755
--- a/docs/content/tools/getfasta.rst
+++ b/docs/content/tools/getfasta.rst
@@ -1,3 +1,5 @@
+.. _getfasta:
+
 ###############
 *getfasta*
 ###############
diff --git a/docs/content/tools/groupby.rst b/docs/content/tools/groupby.rst
index 21aa972a..f28cc92f 100755
--- a/docs/content/tools/groupby.rst
+++ b/docs/content/tools/groupby.rst
@@ -1,3 +1,5 @@
+.. _groupby:
+
 ###############
 *groupby*
 ###############
diff --git a/docs/content/tools/igv.rst b/docs/content/tools/igv.rst
index 2b441894..2f1eb00d 100644
--- a/docs/content/tools/igv.rst
+++ b/docs/content/tools/igv.rst
@@ -1,3 +1,5 @@
+.. _igv:
+
 ###############
 *igv*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/intersect.rst b/docs/content/tools/intersect.rst
index 5fda8b27..735f391c 100755
--- a/docs/content/tools/intersect.rst
+++ b/docs/content/tools/intersect.rst
@@ -1,3 +1,5 @@
+.. _intersect:
+
 #########################################
 *intersect* 
 #########################################
diff --git a/docs/content/tools/jaccard.rst b/docs/content/tools/jaccard.rst
index 3bbf486f..268f945d 100644
--- a/docs/content/tools/jaccard.rst
+++ b/docs/content/tools/jaccard.rst
@@ -1,3 +1,5 @@
+.. _jaccard:
+
 ###############
 *jaccard*
 ###############
diff --git a/docs/content/tools/links.rst b/docs/content/tools/links.rst
index c1be9f14..cbdbee60 100755
--- a/docs/content/tools/links.rst
+++ b/docs/content/tools/links.rst
@@ -1,3 +1,5 @@
+.. _links:
+
 ###############
 *links*
 ###############
diff --git a/docs/content/tools/makewindows.rst b/docs/content/tools/makewindows.rst
index a52fa27b..b95f150f 100644
--- a/docs/content/tools/makewindows.rst
+++ b/docs/content/tools/makewindows.rst
@@ -1,3 +1,5 @@
+.. _makewindows:
+
 ###############
 *makewindows*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/map.rst b/docs/content/tools/map.rst
index b996f952..6ed58f5d 100644
--- a/docs/content/tools/map.rst
+++ b/docs/content/tools/map.rst
@@ -1,3 +1,5 @@
+.. _map:
+
 ###############
 *map*
 ###############
diff --git a/docs/content/tools/maskfasta.rst b/docs/content/tools/maskfasta.rst
index 157844b7..c453aca8 100755
--- a/docs/content/tools/maskfasta.rst
+++ b/docs/content/tools/maskfasta.rst
@@ -1,3 +1,5 @@
+.. _maskfasta:
+
 ###############
 *maskfasta*
 ###############
diff --git a/docs/content/tools/merge.rst b/docs/content/tools/merge.rst
index f41b61a2..e6b35e84 100755
--- a/docs/content/tools/merge.rst
+++ b/docs/content/tools/merge.rst
@@ -1,3 +1,5 @@
+.. _merge:
+
 ###############
 *merge*
 ###############
diff --git a/docs/content/tools/multicov.rst b/docs/content/tools/multicov.rst
index 64dd156e..160461b9 100644
--- a/docs/content/tools/multicov.rst
+++ b/docs/content/tools/multicov.rst
@@ -1,3 +1,5 @@
+.. _multicov:
+
 ###############
 *multicov*
 ###############
@@ -93,4 +95,4 @@ command line.
    chr1	10000	20000	ivl2	123
    chr1	20000	30000	ivl3	213
    chr1	30000	40000	ivl4	335
-   
\ No newline at end of file
+   
diff --git a/docs/content/tools/multiinter.rst b/docs/content/tools/multiinter.rst
index 5578eec7..87cbc6b6 100644
--- a/docs/content/tools/multiinter.rst
+++ b/docs/content/tools/multiinter.rst
@@ -1,3 +1,5 @@
+.. _multiinter:
+
 ###############
 *multiinter*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/nuc.rst b/docs/content/tools/nuc.rst
index 9daad02b..fabe5757 100644
--- a/docs/content/tools/nuc.rst
+++ b/docs/content/tools/nuc.rst
@@ -1,3 +1,5 @@
+.. _nuc:
+
 ###############
 *nuc*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/overlap.rst b/docs/content/tools/overlap.rst
index 6f7a2f57..f365ead4 100755
--- a/docs/content/tools/overlap.rst
+++ b/docs/content/tools/overlap.rst
@@ -1,3 +1,5 @@
+.. _overlap:
+
 ###############
 *overlap*
 ###############
diff --git a/docs/content/tools/pairtobed.rst b/docs/content/tools/pairtobed.rst
index ceae68fb..e872c911 100644
--- a/docs/content/tools/pairtobed.rst
+++ b/docs/content/tools/pairtobed.rst
@@ -1,3 +1,5 @@
+.. _pairtobed:
+
 ###############
 *pairtobed*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/pairtopair.rst b/docs/content/tools/pairtopair.rst
index e286ec11..c4645a8f 100755
--- a/docs/content/tools/pairtopair.rst
+++ b/docs/content/tools/pairtopair.rst
@@ -1,3 +1,5 @@
+.. _pairtopair:
+
 ###############
 *pairtopair*
 ###############
@@ -104,4 +106,4 @@ feature in B.
   
   Result              =====.................................=====
   
-  
\ No newline at end of file
+  
diff --git a/docs/content/tools/random.rst b/docs/content/tools/random.rst
index 7c3a3d39..680d1506 100644
--- a/docs/content/tools/random.rst
+++ b/docs/content/tools/random.rst
@@ -1,3 +1,5 @@
+.. _random:
+
 ###############
 *random*
 ###############
diff --git a/docs/content/tools/reldist.rst b/docs/content/tools/reldist.rst
index b4a55a14..c2698284 100644
--- a/docs/content/tools/reldist.rst
+++ b/docs/content/tools/reldist.rst
@@ -1,3 +1,5 @@
+.. _reldist:
+
 ###############
 *reldist*
 ###############
diff --git a/docs/content/tools/shuffle.rst b/docs/content/tools/shuffle.rst
index 0bde1954..d846e5c2 100755
--- a/docs/content/tools/shuffle.rst
+++ b/docs/content/tools/shuffle.rst
@@ -1,3 +1,5 @@
+.. _shuffle:
+
 ###############
 *shuffle*
 ###############
diff --git a/docs/content/tools/slop.rst b/docs/content/tools/slop.rst
index 1c1ea8df..fb4b9ae3 100755
--- a/docs/content/tools/slop.rst
+++ b/docs/content/tools/slop.rst
@@ -1,3 +1,5 @@
+.. _slop:
+
 ###############
 *slop*
 ###############
diff --git a/docs/content/tools/sort.rst b/docs/content/tools/sort.rst
index 24a01d16..05a4e3aa 100755
--- a/docs/content/tools/sort.rst
+++ b/docs/content/tools/sort.rst
@@ -1,3 +1,5 @@
+.. _sort:
+
 ###############
 *sort*
 ###############
diff --git a/docs/content/tools/subtract.rst b/docs/content/tools/subtract.rst
index 5c05be30..6b1d8082 100755
--- a/docs/content/tools/subtract.rst
+++ b/docs/content/tools/subtract.rst
@@ -1,3 +1,5 @@
+.. _subtract:
+
 ###############
 *subtract*
 ###############
diff --git a/docs/content/tools/tag.rst b/docs/content/tools/tag.rst
index be6ad506..67930327 100644
--- a/docs/content/tools/tag.rst
+++ b/docs/content/tools/tag.rst
@@ -1,3 +1,5 @@
+.. _tag:
+
 ###############
 *tag*
-###############
\ No newline at end of file
+###############
diff --git a/docs/content/tools/unionbedg.rst b/docs/content/tools/unionbedg.rst
index 53819ced..1681324e 100755
--- a/docs/content/tools/unionbedg.rst
+++ b/docs/content/tools/unionbedg.rst
@@ -1,3 +1,5 @@
+.. _unionbg:
+
 ###############
 *unionbedg*
 ###############
@@ -167,4 +169,4 @@ Figure:
   unionBedGraphs -i 1.snp.bg 2.snp.bg 3.snp.bg -filler -/-
   chr1 0 1 A/G C/C A/G
   chr1 5 6 C/T -/- C/T
-  chr1 7 8 -/- T/T -/-
\ No newline at end of file
+  chr1 7 8 -/- T/T -/-
diff --git a/docs/content/tools/window.rst b/docs/content/tools/window.rst
index 38dcfe07..850180fc 100755
--- a/docs/content/tools/window.rst
+++ b/docs/content/tools/window.rst
@@ -1,3 +1,5 @@
+.. _window:
+
 ###############
 *window*
 ###############
-- 
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