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This queue is for tickets about the Bio-SamTools CPAN distribution.

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Id: 98692
Status: open
Priority: 0/
Queue: Bio-SamTools

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Owner: Nobody in particular
Requestors: dietmar.rieder [...] i-med.ac.at
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Subject: Feature request: support for samtools v1.0
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Date: Mon, 08 Sep 2014 13:20:45 +0200
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From: Dietmar Rieder <dietmar.rieder [...] i-med.ac.at>
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It would be great to have support for the uptodate SAMtools version 1.0. I get the following errors when compiling: cc -I/usr/local/bioinf/samtools/src/latest/devel4perl -Ic_bin -I/usr/local/bioinf/perl/perl-5.18.2/lib/5.18.2/x86_64-linux-thread-multi/CORE -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -o c_bin/bam2bedgraph.o c_bin/bam2bedgraph.c c_bin/bam2bedgraph.c:7: error: expected specifier-qualifier-list before ‘samfile_t’ c_bin/bam2bedgraph.c: In function ‘fetch_func’: c_bin/bam2bedgraph.c:13: error: ‘bam_plbuf_t’ undeclared (first use in this function) c_bin/bam2bedgraph.c:13: error: (Each undeclared identifier is reported only once c_bin/bam2bedgraph.c:13: error: for each function it appears in.) c_bin/bam2bedgraph.c:13: error: ‘buf’ undeclared (first use in this function) c_bin/bam2bedgraph.c:13: error: expected expression before ‘)’ token c_bin/bam2bedgraph.c: In function ‘pileup_func’: c_bin/bam2bedgraph.c:29: error: ‘tmpstruct_t’ has no member named ‘in’ c_bin/bam2bedgraph.c: In function ‘main’: c_bin/bam2bedgraph.c:51: error: ‘tmpstruct_t’ has no member named ‘in’ c_bin/bam2bedgraph.c:52: error: ‘tmpstruct_t’ has no member named ‘in’ c_bin/bam2bedgraph.c:57: error: ‘tmpstruct_t’ has no member named ‘in’ c_bin/bam2bedgraph.c:60: error: ‘bam_index_t’ undeclared (first use in this function) c_bin/bam2bedgraph.c:60: error: ‘idx’ undeclared (first use in this function) c_bin/bam2bedgraph.c:61: error: ‘bam_plbuf_t’ undeclared (first use in this function) c_bin/bam2bedgraph.c:61: error: ‘buf’ undeclared (first use in this function) c_bin/bam2bedgraph.c:67: error: ‘tmpstruct_t’ has no member named ‘in’ c_bin/bam2bedgraph.c:73: error: ‘tmpstruct_t’ has no member named ‘in’ c_bin/bam2bedgraph.c:78: error: ‘tmpstruct_t’ has no member named ‘in’ c_bin/bam2bedgraph.c:79: error: ‘tmpstruct_t’ has no member named ‘in’ error building c_bin/bam2bedgraph.o from 'c_bin/bam2bedgraph.c' at /usr/local/bioinf/perl/perl-5.18.2/lib/5.18.2/ExtUtils/CBuilder/Base.pm line 177. LDS/Bio-SamTools-1.39.tar.gz ./Build -- NOT OK Failed during this command: LDS/Bio-SamTools-1.39.tar.gz : make NO When I manually avoid building bam2bedgraph, I get the following error: cc -I/usr/local/bioinf/samtools/src/latest/devel4perl -I/usr/local/bioinf/perl/perl-5.18.2/lib/5.18.2/x86_64-linux-thread-multi/CORE -DVERSION="1.39" -DXS_VERSION="1.39" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -o lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c lib/Bio/DB/Sam.xs: In function ‘XS_Bio__DB__Bam__Alignment_l_aux’: lib/Bio/DB/Sam.xs:575: error: ‘bam1_t’ has no member named ‘l_aux’ lib/Bio/DB/Sam.xs:576: error: ‘bam1_t’ has no member named ‘l_aux’ error building lib/Bio/DB/Sam.o from 'lib/Bio/DB/Sam.c' at /usr/local/bioinf/perl/perl-5.18.2/lib/5.18.2/ExtUtils/CBuilder/Base.pm line 177. Thanks Dietmar
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Any update on this?


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