Clean merge (#115)

* fix bold GFM rendering

Without a space between the *** and the : , Github won't render *** as bold.

* typos?

* Clarify that INFO.VQSLOD is required for --roc

* Update read me with GCC/G++ 4.9.2+ requirement

See #66

* Remove regex dependency + fix test error with gcc 7.3

* Fix Docker build

* Update rtg-tools to work with new Java

* Documentation updates for 0.3.12 release (#110)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Merge doc changes from dev (#112)

* Update RELEASES.md (#87)

* Updated RELASES.md and normalization.md (#109)

* Update more docs (#111)

* Update happy.md

* Cleaned up normalisation.md

* Update happy.md

* Created a new section for working with genome VCFs
  * Added description of --filter-nonref
  * Updated description of --convert-gvcf-xxxx options
  * Added note toward beginning of document calling attention to genome VCF section
* Fixed broken links in TOC
* Fixed inconsistent case in headings

* Resolved merge conflict

* Remove seemingly-unused ENV command

* Restore ENV DEBIAN_FRONTEND=noninteractive

Author: Skola, Dylan

.dockerignore

@@ -24,4 +24,7 @@ compile_commands.json
 tags
 tags_sorted_by_file
 .tags
-.tags_sorted_by_file
+.tags_sorted_by_file
+cmake-build-debug
+cmake-build-release
+build

Dockerfile

@@ -1,4 +1,6 @@
-FROM ubuntu:16.04
+FROM ubuntu:18.04
+
+ENV DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update && \
     apt-get install -y \
@@ -29,7 +31,6 @@ RUN apt-get update && \
         zlib1g-dev && \
     apt-get clean -y
 
-
 RUN pip install bx-python
 
 # copy git repository into the image

Dockerfile.ubuntu-with-tests

@@ -1,4 +1,4 @@
-FROM ubuntu:16.04
+FROM ubuntu:18.04
 
 RUN apt-get update && \
     apt-get install -y \

README.md

@@ -105,7 +105,7 @@ when using variant calling methods that produce many complex variant calls,
 these corner cases can become relevant. Moreover, when benchmarking against
 gold-standard datasets that cover difficult regions of the genome (e.g.
 [Platinum Genomes](http://www.illumina.com/platinumgenomes/)), the more complicated
-subsets of the genome will be respnsible for most of the difference between
+subsets of the genome will be responsible for most of the difference between
 methods.
 
 ### Variant preprocessing
@@ -164,7 +164,7 @@ prefer to combine local haplotypes in the same variant records
 different variant calling methods.
 
 ```
-chr1    201586350       .       CTCTCTCTCT      C
+chr1    201586350       .       CTCTCTCTC       C
 chr1    201586359       .       T               A
 ```
 
@@ -351,7 +351,7 @@ docker build -f Dockerfile.centos6 .
 You will need these tools / libraries on your system to compile the code:
 
 * CMake > 2.8
-* GCC/G++ 4.8+ for compiling
+* GCC/G++ 4.9.2+ for compiling
 * Boost 1.55+
 * Python 2, version 2.7.8 or greater
 * Python packages: Pandas, Numpy, Scipy, pysam, bx-python

doc/happy.md

@@ -48,13 +48,13 @@ are not supported, all input bed or bed.gz files must only contain bed records).
 
 Hap.py will report counts of
 
-*   ***true-positives (TP)***: variants/genotypes that match in truth and query.
-*   ***false-positives (FP)***: variants that have mismatching genotypes or alt
+*   ***true-positives (TP)*** : variants/genotypes that match in truth and query.
+*   ***false-positives (FP)*** : variants that have mismatching genotypes or alt
     alleles, as well as query variant calls in regions a truth set would call
     confident hom-ref regions.
 *   ***false-negatives (FN)*** : variants present in the truth set, but missed
     in the query.
-*   ***non-assessed calls (UNK)***: variants outside the truth set regions
+*   ***non-assessed calls (UNK)*** : variants outside the truth set regions
 
 From these counts, we are able to calculate
 
@@ -488,8 +488,8 @@ a ROC curve based on the query GQX field:
 The `--roc` switch specifies the feature to filter on. Hap.py translates the
 truth and query GQ(X) fields into the INFO fields T_GQ and Q_GQ, it tries to
 use GQX first, if this is not present, it will use GQ. When run without
-internal preprocessing any other input INFO field can be used (e.g. VQSLOD for
-GATK).
+internal preprocessing any other input INFO field can be used (e.g. 
+--roc INFO.VQSLOD for GATK).
 
 The `--roc-filter` switch may be used to specify the particular VCF filter
 which implements a threshold on the quality score. When calculating filtered

example/happy/microbenchmark.sh

@@ -44,7 +44,7 @@ REF=$DIR/hg38.chr21.fa
 # -------
 #
 # To make ROCs for GATK, we discard the LowQual filter and use QUAL
-# For VQSR ROCs, we would use VQSLOD and discard the VQSR Tranche filters
+# For VQSR ROCs, we would use INFO.VQSLOD and discard the VQSR Tranche filters
 
 f=GATK3
 g=${DIR}/NA12878-GATK3-chr21.vcf.gz

src/c++/lib/diploidgraphs/DiploidReference.cpp

@@ -230,6 +230,11 @@ void DiploidReference::setRegion(
                 if(opposite_path != nu_haps.end() && opposite_path != nu_haps.begin())
                 {
                     size_t p2 = opposite_path->second;
+                    // make order reproducible since map is not ordered
+                    if(p2 > p1)
+                    {
+                        std::swap(p1, p2);
+                    }
 
                     nu_haps.erase(nu_haps.begin());
                     nu_haps.erase(opposite_path);

src/c++/lib/quantify/QuantifyRegions.cpp

@@ -41,7 +41,6 @@
 #include "helpers/BCFHelpers.hh"
 
 #include <map>
-#include <regex>
 #include <unordered_map>
 #include <htslib/vcf.h>
 
@@ -102,7 +101,6 @@ namespace variant
     void QuantifyRegions::load(std::vector<std::string> const &rnames, bool fixchr)
     {
         std::unordered_map<std::string, size_t> label_map;
-        const std::regex trailing_number_regex ("(.+)_([0-9]+)$");
         for (std::string const &f : rnames)
         {
             std::vector<std::string> v;
@@ -238,10 +236,22 @@ namespace variant
 
                         if (!fixed_label && v.size() > 3)
                         {
-                            std::smatch string_matches;
-                            if(std::regex_match(v[3], string_matches, trailing_number_regex))
+                            size_t split = v[3].size();
+                            for (size_t pos = v[3].size(); pos != 0; --pos)
                             {
-                                label_ids.insert(getLabelId(label + "_" + string_matches.str(1), 1));
+                                if (v[3][pos] < '0' || v[3][pos] > '9')
+                                {
+                                    break;
+                                }
+                                else
+                                {
+                                    split = pos;
+                                }
+                            }
+
+                            if(split < v[3].size() && v[3][split] == '_')
+                            {
+                                label_ids.insert(getLabelId(label + "_" + v[3].substr(0, split), 1));
                                 label_ids.insert(getLabelId(label + "_" + v[3], 2));
                             }
                             else

src/sh/run_happy_pg_test.sh

@@ -95,7 +95,7 @@ ${PYTHON} ${HCDIR}/hap.py \
 			 	-r ${DIR}/../../example/chr21.fa \
 			 	-o ${TMP_OUT}.unhappy \
 			 	-X --unhappy \
-			 	--roc VQSLOD \
+			 	--roc INFO.VQSLOD \
 			 	--force-interactive
 
 if [[ $? != 0 ]]; then