Closed fizwit closed 6 years ago
Pindel v0.2.5 is from 2013, which was before PR #12 — which made Pindel require only HTSlib, not samtools. And these errors concern bam_header_t
, which was part of the legacy samtools API.
You will not have these errors if you use the most recent release (v0.2.5b8) or current git.
v0.2.5b8 built successfully
gcc 5.4.0 using CPATH to define HTSlib and SAMtools versions 1.8.0
make -C src pindel make[1]: Entering directory
/home/jfdey/sources/pindel-0.2.5/src' g++ -Wall -g -c -O3 -fopenmp -I/app/easybuild/software/HTSlib/1.8-foss-2016b/include/ search_MEI_util.cpp -o search_MEI_util.o search_MEI_util.cpp: In function ‘std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > get_sample_dictionary(bam_header_t*)’: search_MEI_util.cpp:346:17: error: ‘bam_header_t {aka struct bam_hdr_t}’ has no member named ‘dict’ if (header->dict == 0) header->dict = sam_header_parse2(header->text); ^ search_MEI_util.cpp:346:36: error: ‘bam_header_t {aka struct bam_hdr_t}’ has no member named ‘dict’ if (header->dict == 0) header->dict = sam_header_parse2(header->text); ^ search_MEI_util.cpp:357:39: error: ‘bam_header_t {aka struct bam_hdr_t}’ has no member named ‘dict’ tmp_ids = sam_header2list(header->dict, rg_tag, id_tag, &num_ids); ^ search_MEI_util.cpp:359:41: error: ‘bam_header_t {aka struct bam_hdr_t}’ has no member named ‘dict’ tmp_names = sam_header2list(header->dict, rg_tag, sm_tag, &num_names); ^ make[1]: *** [search_MEI_util.o] Error 1 make[1]: Leaving directory
/home/jfdey/sources/pindel-0.2.5/src' make: *** [pindel] Error 2Creating pindel2vcf utility... pindel2vcf created.
Creating sam2pindel utility... sam2pindel created. mv: cannot stat ‘src/pindel’: No such file or directory
Pindel successfully compiled. The pindel executable can be found in this directory.