merge

current_version.txt

@@ -1,3 +1,3 @@
 VERSION_MAJOR 1
 VERSION_MINOR 5
-VERSION_PATCH 0
+VERSION_PATCH 1

doc/source/conf.py

@@ -57,7 +57,7 @@
 # The short X.Y version.
 version = '1.5'
 # The full version, including alpha/beta/rc tags.
-release = '1.5.0'
+release = '1.5.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docker/Dockerfile

@@ -6,7 +6,7 @@ MAINTAINER salmon.maintainer@gmail.com
 
 ENV PACKAGES git gcc make g++ libboost-all-dev liblzma-dev libbz2-dev \
     ca-certificates zlib1g-dev libcurl4-openssl-dev curl unzip autoconf apt-transport-https ca-certificates gnupg software-properties-common wget
-ENV SALMON_VERSION 1.5.0
+ENV SALMON_VERSION 1.5.1
 
 # salmon binary will be installed in /home/salmon/bin/salmon
 

docker/build_test.sh

@@ -1,3 +1,3 @@
 #! /bin/bash
-SALMON_VERSION=1.5.0
+SALMON_VERSION=1.5.1
 docker build --no-cache -t combinelab/salmon:${SALMON_VERSION} -t combinelab/salmon:latest .

include/SalmonConfig.hpp

@@ -27,8 +27,8 @@
 namespace salmon {
 constexpr char majorVersion[] = "1";
 constexpr char minorVersion[] = "5";
-constexpr char patchVersion[] = "0";
-constexpr char version[] = "1.5.0";
+constexpr char patchVersion[] = "1";
+constexpr char version[] = "1.5.1";
 constexpr uint32_t indexVersion = 5;
 constexpr char requiredQuasiIndexVersion[] = "p7";
 } // namespace salmon

include/SingleCellProtocols.hpp

@@ -101,10 +101,13 @@ namespace alevin{
         maxValue(maxValue_){
         alevin::types::AlevinUMIKmer::k(umiLength);
       }
-      // NOTE: these do nothing but satisfy 
-      // template requirements right now
-      void set_umi_geo(TagGeometry& g) { umiLength = g.length1 + g.length2; };
-      void set_bc_geo(TagGeometry& g) { barcodeLength = g.length1 + g.length2; };
+      // NOTE: these functions are duplicated 
+      // with those in `CustomGeometry` below, and 
+      // due to semantics have slightly different 
+      // implementations. See if the design can be 
+      // unified later.
+      void set_umi_geo(TagGeometry& g) { umiLength = g.length(); };
+      void set_bc_geo(TagGeometry& g) { barcodeLength = g.length(); };
       void set_read_geo(TagGeometry& g) { (void)g; };
       uint32_t barcode_length() const { return barcodeLength; }
       uint32_t umi_length() const { return umiLength; }
@@ -185,14 +188,15 @@ namespace alevin{
       TagGeometry bc_geo;
       TagGeometry read_geo;
 
-      void set_umi_geo(TagGeometry& g) { umi_geo = g; umiLength = umi_geo.length1 + umi_geo.length2; }
-      void set_bc_geo(TagGeometry& g) { bc_geo = g; barcodeLength = bc_geo.length1 + bc_geo.length2; }
+      void set_umi_geo(TagGeometry& g) { umi_geo = g; umiLength = umi_geo.length(); }
+      void set_bc_geo(TagGeometry& g) { bc_geo = g; barcodeLength = bc_geo.length(); }
       void set_read_geo(TagGeometry& g) { read_geo = g; }
       uint32_t barcode_length() const { return barcodeLength; }
       uint32_t umi_length() const { return umiLength; }
 
-      // These values do nothing in this class except
-      // maintain template compat ... fix this design later.
+      // These values are set only when `set_umi_geo` and 
+      // `set_bc_geo` are called.  See if this design can 
+      // be better integrated with `Rule` later.
       uint32_t barcodeLength, umiLength, maxValue;
       BarcodeEnd end;
     };