| Subject: | Feature request: support for samtools v1.0 |
| Date: | Mon, 08 Sep 2014 13:20:45 +0200 |
| To: | bug-Bio-SamTools [...] rt.cpan.org |
| From: | Dietmar Rieder <dietmar.rieder [...] i-med.ac.at> |
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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