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biology/vt: Patch to work with htslib 1.10.2

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Minor API changes requiring type casts
This commit is contained in:
Jason W. Bacon 2020-08-03 17:42:32 +00:00
parent fb3f006dcf
commit 551f57c4e0
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=544091
5 changed files with 62 additions and 1 deletions
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3
biology/vt/Makefile
View file

@ -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

20
biology/vt/files/patch-bcf__ordered__writer.cpp Normal file
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@ -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)
{

11
biology/vt/files/patch-discover.cpp Normal file
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@ -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

11
biology/vt/files/patch-genotype.cpp Normal file
View file

@ -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

18
biology/vt/files/patch-read__filter.cpp Normal file
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@ -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
+}