5 files changed, 62 insertions, 1 deletions

diff --git a/biology/vt/Makefile b/biology/vt/Makefile
index bc41eccadc31..f4fcf29ae15f 100644
--- a/biology/vt/Makefile
+++ b/biology/vt/Makefile
@@ -2,6 +2,7 @@
 
 PORTNAME=	vt
 DISTVERSION=	0.57721
+PORTREVISION=	1
 CATEGORIES=	biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -9,7 +10,7 @@ COMMENT=	Discovers short variants from Next Generation Sequencing data
 
 LICENSE=	MIT
 
-LIB_DEPENDS=	libhts.so:biology/htslib \
+LIB_DEPENDS=	libhts.so.3:biology/htslib \
 		libsvm.so:science/libsvm \
 		libdeflate.so:archivers/libdeflate \
 		libcurl.so:ftp/curl
diff --git a/biology/vt/files/patch-bcf__ordered__writer.cpp b/biology/vt/files/patch-bcf__ordered__writer.cpp
new file mode 100644
index 000000000000..ff58990bb063
--- /dev/null
+++ b/biology/vt/files/patch-bcf__ordered__writer.cpp
@@ -0,0 +1,20 @@
+--- bcf_ordered_writer.cpp.orig	2020-07-27 13:12:44 UTC
++++ bcf_ordered_writer.cpp
+@@ -155,7 +155,7 @@ void BCFOrderedWriter::write(bcf1_t *v)
+ 
+                 if (i==buffer.end())
+                 {
+-                    int32_t cutoff_pos1 =  std::max(bcf_get_pos1(buffer.front())-window,1);
++                    int32_t cutoff_pos1 =  std::max(bcf_get_pos1(buffer.front())-window,(hts_pos_t)1);
+                     if (bcf_get_pos1(v)<cutoff_pos1)
+                     {
+                         fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n",
+@@ -251,7 +251,7 @@ void BCFOrderedWriter::flush(bool force)
+     {
+         if (buffer.size()>1)
+         {
+-            int32_t cutoff_pos1 =  std::max(bcf_get_pos1(buffer.front())-window,1);
++            int32_t cutoff_pos1 =  std::max(bcf_get_pos1(buffer.front())-window,(hts_pos_t)1);
+ 
+             while (buffer.size()>1)
+             {
diff --git a/biology/vt/files/patch-discover.cpp b/biology/vt/files/patch-discover.cpp
new file mode 100644
index 000000000000..432638c9ce27
--- /dev/null
+++ b/biology/vt/files/patch-discover.cpp
@@ -0,0 +1,11 @@
+--- discover.cpp.orig	2020-07-27 13:45:38 UTC
++++ discover.cpp
+@@ -352,7 +352,7 @@ class Igor : Program
+                             //already present
+                             free(qname);
+                         }
+-                        kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1};
++                        kh_val(reads, k) = {(int32_t)bam_get_pos1(s), (int32_t)bam_get_pos1(s)+bam_get_l_qseq(s)-1};
+                     }
+                 }
+                 else
diff --git a/biology/vt/files/patch-genotype.cpp b/biology/vt/files/patch-genotype.cpp
new file mode 100644
index 000000000000..2cce36b46fbe
--- /dev/null
+++ b/biology/vt/files/patch-genotype.cpp
@@ -0,0 +1,11 @@
+--- genotype.cpp.orig	2020-07-27 13:47:27 UTC
++++ genotype.cpp
+@@ -301,7 +301,7 @@ class Igor : Program
+                             //already present
+                             free(qname);
+                         }
+-                        kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1};
++                        kh_val(reads, k) = {(int32_t)bam_get_pos1(s), (int32_t)bam_get_pos1(s)+bam_get_l_qseq(s)-1};
+                     }
+                 }
+                 else
diff --git a/biology/vt/files/patch-read__filter.cpp b/biology/vt/files/patch-read__filter.cpp
new file mode 100644
index 000000000000..3496945d575a
--- /dev/null
+++ b/biology/vt/files/patch-read__filter.cpp
@@ -0,0 +1,18 @@
+--- read_filter.cpp.orig	2020-07-27 13:49:14 UTC
++++ read_filter.cpp
+@@ -92,7 +92,7 @@ bool ReadFilter::filter_read(bam_hdr_t* h, bam1_t *s)
+                         //already present
+                         free(qname);
+                     }
+-                    kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1};
++                    kh_val(reads, k) = {(int32_t)bam_get_pos1(s), (int32_t)bam_get_pos1(s)+bam_get_l_qseq(s)-1};
+                 }
+             }
+             else
+@@ -272,4 +272,4 @@ void ReadFilter::bam_print_key_values(bam_hdr_t *h, ba
+     if (qual.m) free(qual.s);
+     if (cigar_string.m) free(cigar_string.s);
+     if (cigar_expanded_string.m) free(cigar_expanded_string.s);
+-}
+\ No newline at end of file
++}