Merge branch 'hotfix-contact'

closes issue #15

Author: yannickspill

CHANGELOG.md

@@ -4,6 +4,11 @@ All notable changes to *binless* will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 for versions 0.x of binless, minor releases might break backwards compatibility.
 
+## [0.15.1]
+### Fixed
+- bug arising when a particular locus does not have reads in at least one
+  contact category
+
 ## [0.15.0]
 ### Added
 - less errors regarding documentation when compiling
@@ -134,7 +139,8 @@ for versions 0.x of binless, minor releases might break backwards compatibility.
 - Initial commit
 
 
-[0.15.0]: ../../compare/v0.14.0...HEAD
+[0.15.1]: ../../compare/v0.15.0...HEAD
+[0.15.0]: ../../compare/v0.14.0...v0.15.0
 [0.14.0]: ../../compare/v0.13.0...v0.14.0
 [0.13.0]: ../../compare/v0.12.0...v0.13.0
 [0.12.0]: ../../compare/v0.11.0...v0.12.0

binless/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: binless
 Type: Package
 Title: binless: Resolution-independent Normalization And Interaction Detection For Hi-C Data
-Version: 0.15.0
+Version: 0.15.1
 Authors@R: person("Yannick", "Spill", email = "yannick.spill@nsup.org", role = c("aut", "cre"))
 Author: Yannick Spill [aut, cre]
 Maintainer: Yannick Spill <yannick.spill@nsup.org>

binless/R/preprocess.R

@@ -244,10 +244,15 @@ prepare_for_sparse_cs_norm = function(data, both=F, circularize=-1) {
   stopifnot(all(X[,id==.I])) #IDs must start at one and have no gaps, for current stan implementation
   #
   cat("Produce count list\n")
+  contact.names = c("contact.close", "contact.down", "contact.far", "contact.up")
   Y=dcast.data.table(enrich[id1 != id2 
-                            & category %in% c("contact.close", "contact.down", "contact.far", "contact.up"),
+                            & category %in% contact.names,
                             .(id1,id2,pos1=re.closest1,pos2=re.closest2,category,N)],
                      ...~category, value.var="N", fill=0)
+  if (!all(contact.names %in% colnames(Y))) {
+    missing <- contact.names[!contact.names %in% colnames(Y)]
+    Y[,missing] <- 0
+  }
   setkey(Y,id1,id2)
   Y[,distance:=pos2-pos1]
   if (circularize>0) Y[,distance:=pmin(distance,circularize-distance+1)]