svn commit: r544091 - in head/biology/vt: . files
Jason W. Bacon
jwb at FreeBSD.org
Mon Aug 3 17:42:34 UTC 2020
Author: jwb
Date: Mon Aug 3 17:42:32 2020
New Revision: 544091
URL: https://svnweb.freebsd.org/changeset/ports/544091
Log:
biology/vt: Patch to work with htslib 1.10.2
Minor API changes requiring type casts
Added:
head/biology/vt/files/patch-bcf__ordered__writer.cpp (contents, props changed)
head/biology/vt/files/patch-discover.cpp (contents, props changed)
head/biology/vt/files/patch-genotype.cpp (contents, props changed)
head/biology/vt/files/patch-read__filter.cpp (contents, props changed)
Modified:
head/biology/vt/Makefile
Modified: head/biology/vt/Makefile
==============================================================================
--- head/biology/vt/Makefile Mon Aug 3 17:40:04 2020 (r544090)
+++ head/biology/vt/Makefile Mon Aug 3 17:42:32 2020 (r544091)
@@ -2,6 +2,7 @@
PORTNAME= vt
DISTVERSION= 0.57721
+PORTREVISION= 1
CATEGORIES= biology
MAINTAINER= jwb at FreeBSD.org
@@ -9,7 +10,7 @@ COMMENT= Discovers short variants from Next Generation
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
Added: head/biology/vt/files/patch-bcf__ordered__writer.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/vt/files/patch-bcf__ordered__writer.cpp Mon Aug 3 17:42:32 2020 (r544091)
@@ -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)
+ {
Added: head/biology/vt/files/patch-discover.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/vt/files/patch-discover.cpp Mon Aug 3 17:42:32 2020 (r544091)
@@ -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
Added: head/biology/vt/files/patch-genotype.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/vt/files/patch-genotype.cpp Mon Aug 3 17:42:32 2020 (r544091)
@@ -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
Added: head/biology/vt/files/patch-read__filter.cpp
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/vt/files/patch-read__filter.cpp Mon Aug 3 17:42:32 2020 (r544091)
@@ -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
++}
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