Date: Mon, 3 Aug 2020 17:42:32 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r544091 - in head/biology/vt: . files Message-ID: <202008031742.073HgWx6040039@repo.freebsd.org>
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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@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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