add contiguous .id to bed_merge example (#171)

- update news - roxygen bump - re-pkg
rnabioco · Mar 1, 2017 · d9545f4 · d9545f4
1 parent 772ee26
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -36,6 +36,6 @@ Suggests:
     RMySQL,
     purrr
 VignetteBuilder: knitr
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
 URL: http://github.com/rnabioco/valr/
 BugReports: https://github.com/rnabioco/valr/issues
diff --git a/NEWS.md b/NEWS.md
@@ -1,11 +1,13 @@
-# valr 0.1.2
+# valr 0.1.2 (unreleased)
 
 ## Major changes
 
 * Deprecate `bed_sort()` in favor of using `dplyr::arrange()` explicitly (fixes #134).
 
 ## Minor changes
 
+* Make `.id` values contiguous values in `bed_cluster()` output (#171)
+
 * Transfer repository to http:://github.com/rnabioco/valr, update links and docs.
 
 * Move shiny app to new repo (http://github.com/rnabioco/valrdata).

diff --git a/R/bed_cluster.r b/R/bed_cluster.r
@@ -21,7 +21,9 @@
 #'  "chr1", 100,  200,
 #'  "chr1", 180,  250,
 #'  "chr1", 250,  500,
-#'  "chr1", 501,  1000
+#'  "chr1", 501,  1000,
+#'  "chr2", 1,    100,
+#'  "chr2", 150,  200
 #' )
 #'
 #' bed_cluster(x)

diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/reference/bed_cluster-4.png b/docs/reference/bed_cluster-4.png
diff --git a/docs/reference/bed_cluster.html b/docs/reference/bed_cluster.html
diff --git a/docs/reference/bed_flank-2.png b/docs/reference/bed_flank-2.png
diff --git a/docs/reference/bed_glyph-4.png b/docs/reference/bed_glyph-4.png
diff --git a/docs/reference/bed_glyph-6.png b/docs/reference/bed_glyph-6.png
diff --git a/docs/reference/bed_makewindows-2.png b/docs/reference/bed_makewindows-2.png
diff --git a/docs/reference/bed_merge-2.png b/docs/reference/bed_merge-2.png
diff --git a/docs/reference/bed_merge.html b/docs/reference/bed_merge.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/man/bed12_to_exons.Rd b/man/bed12_to_exons.Rd
diff --git a/man/bed_absdist.Rd b/man/bed_absdist.Rd
diff --git a/man/bed_closest.Rd b/man/bed_closest.Rd
diff --git a/man/bed_cluster.Rd b/man/bed_cluster.Rd
diff --git a/man/bed_complement.Rd b/man/bed_complement.Rd
diff --git a/man/bed_coverage.Rd b/man/bed_coverage.Rd
diff --git a/man/bed_fisher.Rd b/man/bed_fisher.Rd
diff --git a/man/bed_flank.Rd b/man/bed_flank.Rd
diff --git a/man/bed_glyph.Rd b/man/bed_glyph.Rd
diff --git a/man/bed_intersect.Rd b/man/bed_intersect.Rd
diff --git a/man/bed_jaccard.Rd b/man/bed_jaccard.Rd
diff --git a/man/bed_makewindows.Rd b/man/bed_makewindows.Rd
diff --git a/man/bed_map.Rd b/man/bed_map.Rd
diff --git a/man/bed_merge.Rd b/man/bed_merge.Rd
diff --git a/man/bed_projection.Rd b/man/bed_projection.Rd
diff --git a/man/bed_random.Rd b/man/bed_random.Rd
diff --git a/man/bed_reldist.Rd b/man/bed_reldist.Rd
diff --git a/man/bed_shift.Rd b/man/bed_shift.Rd
diff --git a/man/bed_shuffle.Rd b/man/bed_shuffle.Rd
diff --git a/man/bed_slop.Rd b/man/bed_slop.Rd
diff --git a/man/bed_sort.Rd b/man/bed_sort.Rd
diff --git a/man/bed_subtract.Rd b/man/bed_subtract.Rd
diff --git a/man/bed_window.Rd b/man/bed_window.Rd
diff --git a/man/bound_intervals.Rd b/man/bound_intervals.Rd
diff --git a/man/db.Rd b/man/db.Rd
diff --git a/man/flip_strands.Rd b/man/flip_strands.Rd
diff --git a/man/interval_spacing.Rd b/man/interval_spacing.Rd
diff --git a/man/read_bed.Rd b/man/read_bed.Rd
diff --git a/man/read_genome.Rd b/man/read_genome.Rd
diff --git a/man/read_vcf.Rd b/man/read_vcf.Rd
diff --git a/man/sorting.Rd b/man/sorting.Rd