Index: head/biology/haplohseq/Makefile
===================================================================
--- head/biology/haplohseq/Makefile	(revision 517827)
+++ head/biology/haplohseq/Makefile	(revision 517828)
@@ -1,29 +1,34 @@
 # $FreeBSD$
 
 PORTNAME=	haplohseq
 DISTVERSION=	0.1.2
+PORTREVISION=	1
 CATEGORIES=	biology
-MASTER_SITES=	https://mirror1.hpc.uwm.edu/Distfiles/ \
-		https://mirror2.hpc.uwm.edu/Distfiles/
-DISTNAME=	haplohseq_source-${DISTVERSION}
+MASTER_SITES=	https://acadix.biz/Ports/distfiles/
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Identify regions of allelic imbalance
 
 LICENSE=	MIT
 
 LIB_DEPENDS=	libboost_system.so:devel/boost-libs
+RUN_DEPENDS=	R-cran-optparse>0:devel/R-cran-optparse
 
-USES=		compiler:c++11-lang gmake localbase:ldflags zip
+USES=		compiler:c++11-lang gmake localbase:ldflags python:2.7 tar:xz
 
+OPTIONS_DEFINE=	EXAMPLES
+
 MAKEFILE=	makefile
-WRKSRC=		${WRKDIR}/haplohseq_source
 LDFLAGS+=	-lpthread
 MAKE_ENV=	STRIP=${STRIP}
 
-PLIST_FILES=	bin/haplohseq
+SUB_FILES=	haplohseq-example
+
+post-install-EXAMPLES-on:
+	${INSTALL_SCRIPT} ${WRKDIR}/haplohseq-example ${STAGEDIR}${PREFIX}/bin
+	(cd ${WRKSRC} && ${COPYTREE_SHARE} "example ldmap scripts" ${STAGEDIR}${EXAMPLESDIR})
 
 do-test:
 	@(cd ${WRKSRC}/build/test && ${FILESDIR}/run-tests)
 
 .include <bsd.port.mk>
Index: head/biology/haplohseq/distinfo
===================================================================
--- head/biology/haplohseq/distinfo	(revision 517827)
+++ head/biology/haplohseq/distinfo	(revision 517828)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1567118170
-SHA256 (haplohseq_source-0.1.2.zip) = 35f8fe6718020e6eacdc309d28fc5dd3cc7c6e8400da1d962fdf6fb52d4e90c5
-SIZE (haplohseq_source-0.1.2.zip) = 63620
+TIMESTAMP = 1573660978
+SHA256 (haplohseq-0.1.2.tar.xz) = 0e7474f6af6b41c4b38f5f4549344714ec022e2adfc4aa9d00e0d420483e260a
+SIZE (haplohseq-0.1.2.tar.xz) = 8108896
Index: head/biology/haplohseq/files/haplohseq-example.in
===================================================================
--- head/biology/haplohseq/files/haplohseq-example.in	(nonexistent)
+++ head/biology/haplohseq/files/haplohseq-example.in	(revision 517828)
@@ -0,0 +1,37 @@
+#!/bin/sh -e
+
+##########################################################################
+#   Script description:
+#       Run haplohseq example
+#
+#   https://sites.google.com/site/integrativecancergenomics/software/haplohseq
+#       
+#   History:
+#   Date        Name        Modification
+#   2019-11-13  Jason Bacon Begin
+##########################################################################
+
+usage()
+{
+    printf "Usage: $0 directory\n"
+    exit 1
+}
+
+
+##########################################################################
+#   Main
+##########################################################################
+
+if [ $# != 1 ]; then
+    usage
+fi
+
+dir="$1"
+
+if [ -e "$dir" ]; then
+    printf "'$dir' already exists.  Please remove it or specify another.\n"
+    exit 1
+fi
+cp -R %%EXAMPLESDIR%% "$dir"
+cd "$dir/example"
+sh ./example_run.sh

Property changes on: head/biology/haplohseq/files/haplohseq-example.in
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Index: head/biology/haplohseq/files/patch-example_example__run.sh
===================================================================
--- head/biology/haplohseq/files/patch-example_example__run.sh	(nonexistent)
+++ head/biology/haplohseq/files/patch-example_example__run.sh	(revision 517828)
@@ -0,0 +1,24 @@
+--- example/example_run.sh.orig	2019-11-13 15:45:57 UTC
++++ example/example_run.sh
+@@ -1,4 +1,4 @@
+-#! /bin/bash
++#!/bin/sh
+ 
+ # Example:
+ # Identify allelic imbalance (AI) given a tumor 
+@@ -6,13 +6,13 @@
+ # of the GATK.  This involves the following 3 steps.
+ 
+ printf "STEP 1: PHASING 1KG HET SITES ...\n"
+-python ../scripts/simple_phaser.py \
++python2.7 ../scripts/simple_phaser.py \
+   --ldmap ../ldmap/hg19.exome.ldmap \
+   --vcf example_input/tumor_exome.vcf \
+   -o example_output/tumor_exome
+ 
+ printf "\nSTEP 2: IDENTIFYING REGIONS OF AI ...\n"
+-../haplohseq \
++haplohseq \
+   --vcf example_output/tumor_exome.hap.vcf \
+   --phased example_output/tumor_exome.hap \
+   --event_prevalence 0.1 \

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Index: head/biology/haplohseq/files/patch-scripts_ldmap.py
===================================================================
--- head/biology/haplohseq/files/patch-scripts_ldmap.py	(nonexistent)
+++ head/biology/haplohseq/files/patch-scripts_ldmap.py	(revision 517828)
@@ -0,0 +1,8 @@
+--- scripts/ldmap.py.orig	2019-11-13 15:51:02 UTC
++++ scripts/ldmap.py
+@@ -1,3 +1,5 @@
++#!/usr/bin/env python2.7
++
+ import argparse
+ import sys
+ import random

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Index: head/biology/haplohseq/files/patch-scripts_simple__phaser.py
===================================================================
--- head/biology/haplohseq/files/patch-scripts_simple__phaser.py	(nonexistent)
+++ head/biology/haplohseq/files/patch-scripts_simple__phaser.py	(revision 517828)
@@ -0,0 +1,8 @@
+--- scripts/simple_phaser.py.orig	2019-11-13 15:52:02 UTC
++++ scripts/simple_phaser.py
+@@ -1,3 +1,5 @@
++#!/usr/bin/env python2.7
++
+ import argparse
+ import random
+ import sys

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Index: head/biology/haplohseq/files/patch-src_FreqPhase.cpp
===================================================================
--- head/biology/haplohseq/files/patch-src_FreqPhase.cpp	(nonexistent)
+++ head/biology/haplohseq/files/patch-src_FreqPhase.cpp	(revision 517828)
@@ -0,0 +1,29 @@
+--- src/FreqPhase.cpp.orig	2019-11-13 14:19:06 UTC
++++ src/FreqPhase.cpp
+@@ -5,6 +5,7 @@
+  * Email:  sanlucas@gmail.com
+  */
+ 
++#include <sysexits.h>
+ #include "FreqPhase.h"
+ 
+ namespace haplohseq {
+@@ -180,10 +181,17 @@ double FreqPhase::meanValue(const std::v
+ double FreqPhase::medianValue(const std::vector<double>& values) {
+ 	double median;
+ 	size_t size = values.size();
++
++	// We can probably detect this condition earlier while loading the VCF
++	if ( size == 0 ) {
++		std::cerr << "FreqPhase::medianValue(): values vector is empty." << std::endl;
++		std::cerr << "Make sure your VCF has all of GT:AD:DP in the FORMAT column." << std::endl;
++		exit(EX_DATAERR);
++	}
+ 	std::vector<double> tempFreqs(values);
+ 	sort(tempFreqs.begin(), tempFreqs.end());
+ 
+-	if (size  % 2 == 0) {
++	if (size % 2 == 0) {
+ 		median = (tempFreqs[size / 2 - 1] + tempFreqs[size / 2]) / 2;
+ 	}
+ 	else {

Property changes on: head/biology/haplohseq/files/patch-src_FreqPhase.cpp
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Index: head/biology/haplohseq/pkg-plist
===================================================================
--- head/biology/haplohseq/pkg-plist	(nonexistent)
+++ head/biology/haplohseq/pkg-plist	(revision 517828)
@@ -0,0 +1,11 @@
+bin/haplohseq
+%%PORTEXAMPLES%%bin/haplohseq-example
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/example/example_input/tumor_exome.vcf
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/example/example_run.sh
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ldmap/hg19.exome.ldmap
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/haplohseq_plot.R
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/ldmap.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/ldmap.py.orig
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/simple_phaser.py
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scripts/simple_phaser.py.orig
+%%PORTEXAMPLES%%@dir %%EXAMPLESDIR%%/example/example_output

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