grenaud / glactools Goto Github PK

Hello.

I have a problem using vcfm2acf.

glactools vcfm2acf --onlyGT --fai human_g1k_v37.fasta.fai chr1.recode.vcf > chr1.acf.gz

error message
libgab.h base2int() Invalid base *

Please let me know if any improvements can be made.

Thanks.

Hi,
I want to know whether bam2acf only accepts one bam file as input, how about multiple samples bam files of a population, how to deal with this?

Hi,

I am converting a multi-sample VCF file to glactools acf format and I am using the --onlyGT flag since my VCF contains only genotypes. Weirdly, when I remove this flag, glactools still runs and outputs a file even though I have checked and confirmed there are no PL fields in my VCF...

grep "##FORMAT=" ALLchr_CEUlist_concat.vcf
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

Does glactools interpret that a VCF contains only genotypes without the need for --onlyGT or am I misunderstanding the flag? Based on the comment in Vcf2ACF.cpp I assumed that glactools uses the PL field which is not present in my VCF.

Best,

Dean

Hi, I am currently trying to convert a VCF file to an ACF file using glactools. However, I have encountered the following error message:

Error, missing data in the EPO file
Error: GlacParser tried to read 4 bytes but got 0

I tried the solution in another issue. I've rewritten "chr22" as "22". However, this allowed some chromosomes to run smoothly, while others still reported errors.

Error, missing data in the EPO file
Warning: No EOF marker, likely due to an I/O error
Error: GlacParser tried to read 2 bytes but got 0

I wonder if you have any suggestions for this? By the way, my variants were mapped to hg38 rather than hg19/37. Could this be the cause of the error message? Looking forward to your reply, thank you!

Hi,
I used glactools to convert multiple sample vcf file to acf format and finally treemix format
./glactools vcfm2acf --fai ../data/Camarosa_CMN_genomes.fasta.fai ../DoB_rand_samples_CallVariants.vcf
Unfortunately, there was an error
SimpleVCF: unable to determine genotype for field=#0/0/0/0/0/0/0/0# at position: Fvb1-1:7753

The vcf file I used is made from callvariants, which is a script in bbmap.
Besides, I tried to get acf file from bam formate. I also failed with the following report.

./glactools bam2acf ../data/Camarosa_CMN_genomes.fasta ../virg_NA-UT-2-6-3.realigned.bam virg_NA-UT-2-6-3
� � BC� 48m�UU�( 6����in�;.R
H(bwwk}9�yg;�k̹r>U)RZEv�D|Z4ټeҪyTkޱyݛ7Vn;uغ{6ͻh�uծ[fukҸ\frY廵nޡ]N[�J�s�5k5nZaZV**?ey3rZfgʫѦu
-ZTo:?b4�W/W!\�U4W�ߨAFu+"\Fu+eggVdR1?Bn^6e&;+7'7��Ɏ%bżrrsfV_켊���+'B^V7?3'r
K_/VN~n -3��r*V:lSBVvœd7'3?'䨜 m9Y_1#_ONǒ
AAg%LdṰX9Y9A97�ONFV^^n�bddeE[Hǻ�oٹsVQJŻuܣxN-�W%DW�eT
[E::bgzf_flush] File write failed (wrong size)
Write error
BAM2ACF: error writing header

May I have some help from anybody? Thanks!

Dear Gabriel,

I'm receiving the following error when attempting to use replaceanc:
$ glactools replaceanc chr1.pops.acf.gz chr1.ancroot.acf.gz > ancrooted.chr1.acf.gz

GlacReplaceAncestor: The SQ fields differ in the header, are they from the same reference?

Is there a way to override or force glactools to accept that the references are the same, or to use one over the other? The reference genomes I used were the same sequences, but with differing sequence names - I had to shorten the names whilst generating the ancestral and root vcfs and that may be causing this issue downstream.

Failing that, is there a way to manually edit the headers of acf files?

Cheers

Cooper

it shows: Program acf2treemix wrote 0 out of 5733 terminated gracefully
I used
glactools bplink2acf --fai refer.fai plink_prefix | glactools acf2treemix - | gzip >plink_prefix.gz

does the input data need to be extra modification?
By the way, how many sites are needed to run treemix at least? I found out that not many sno left after using 'geno 0' in plink? Afraid to use this tool in the wrong way?

Hi ,
The commond line of program 'usepopsrootanc'
glactools usepopsrootanc [options]
What is the format of file ? the glac file contains root and ancestral samples?
Thanks!

Hi,

Thanks for the grear program. It looks like I cannot use bed track with glactools bam2acf:

$ glactools bam2acf --bed $bed $ref_fa $bam test | glactools view - | cut -f 1-3,6

The last 3 arguments are
Error: GlacParser tried to read 4 bytes but got 0

But, I can run it without a bed track. My bed track looks like this:

1 11204715 11204717
17 7578460 7578461
17 15978895 15978897

Thanks,

Jack

Hey grenaud,

I am getting an empty output for acf2betascan:

glactools acf2betascan --useanc ../acf_files/APHP_holi13.acf > APHP_beta.freq

it seems to have run fine:
Program ACF2BETASCAN looked at 5171179 records, terminated gracefully

Any ideas?

Thanks!

Hello Gabriel,
Here is the compilation output I get when I tried to compile on Mac Mojave v. 10.14.4
Peter

uhtred:glactools-master bgppermp$ make
rm -rf bamtools/
git clone --recursive https://github.com/pezmaster31/bamtools.git
Cloning into 'bamtools'...
remote: Enumerating objects: 4857, done.
remote: Total 4857 (delta 0), reused 0 (delta 0), pack-reused 4857
Receiving objects: 100% (4857/4857), 6.06 MiB | 8.05 MiB/s, done.
Resolving deltas: 100% (3373/3373), done.
cd bamtools/ && mkdir -p build/ && cd build/ && cmake .. && make && cd ../..
-- The CXX compiler identification is AppleClang 10.0.1.10010046
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at CMakeLists.txt:20 (cmake_policy):
The OLD behavior for policy CMP0042 will be removed from a future version
of CMake.

The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.

-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")
-- Checking for one of the modules 'jsoncpp>=1'
Did NOT find system JsonCpp, instead using bundled version
-- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.11")
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/bgppermp/Downloads/glactools-master/bamtools/build
Scanning dependencies of target SharedHeaders
[ 0%] Built target SharedHeaders
Scanning dependencies of target APIHeaders
[ 0%] Built target APIHeaders
Scanning dependencies of target AlgorithmsHeaders
[ 0%] Built target AlgorithmsHeaders
Scanning dependencies of target BamTools
[ 1%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o
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[ 62%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
[ 63%] Linking CXX static library libbamtools.a
[ 63%] Built target BamTools
Scanning dependencies of target jsoncpp
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[ 67%] Linking CXX static library libjsoncpp.a
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Scanning dependencies of target BamTools-utils
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Scanning dependencies of target bamtools_cmd
[ 77%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o
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[100%] Linking CXX executable bamtools
[100%] Built target bamtools_cmd
rm -rf htslib/
git clone --recursive https://github.com/samtools/htslib.git
Cloning into 'htslib'...
remote: Enumerating objects: 10, done.
remote: Counting objects: 100% (10/10), done.
remote: Compressing objects: 100% (10/10), done.
remote: Total 11614 (delta 1), reused 3 (delta 0), pack-reused 11604
Receiving objects: 100% (11614/11614), 8.50 MiB | 6.15 MiB/s, done.
Resolving deltas: 100% (8214/8214), done.
cd htslib/ && make && cd ../
echo '/* Default config.h generated by Makefile /' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
echo '#define HAVE_LIBCURL 1' >> config.h
gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I. -c -o errmod.o errmod.c
gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I. -c -o header.o header.c
gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.9-288-g830c061"' > version.h
gcc -g -Wall -O2 -I. -c -o hts.o hts.c
gcc -g -Wall -O2 -I. -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -I. -c -o md5.o md5.c
gcc -g -Wall -O2 -I. -c -o multipart.o multipart.c
gcc -g -Wall -O2 -I. -c -o probaln.o probaln.c
gcc -g -Wall -O2 -I. -c -o realn.o realn.c
gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c
gcc -g -Wall -O2 -I. -c -o region.o region.c
gcc -g -Wall -O2 -I. -c -o sam.o sam.c
gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I. -c -o textutils.o textutils.c
gcc -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -I. -c -o hfile_libcurl.o hfile_libcurl.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o hfile_libcurl.o
ranlib libhts.a
gcc -dynamiclib -install_name /usr/local/lib/libhts.2to3part10.dylib -current_version 1.9.255 -compatibility_version 2.10 -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o hfile_libcurl.o -lz -lm -lbz2 -llzma -lcurl
ln -sf libhts.dylib libhts.2to3part10.dylib
gcc -g -Wall -O2 -I. -c -o bgzip.o bgzip.c
gcc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o htsfile.o htsfile.c
gcc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o tabix.o tabix.c
gcc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/hts_endian.o test/hts_endian.c
gcc -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma -lcurl
gcc -g -Wall -O2 -I. -c -o test/fieldarith.o test/fieldarith.c
gcc -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/hfile.o test/hfile.c
gcc -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/pileup.o test/pileup.c
gcc -o test/pileup test/pileup.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/sam.o test/sam.c
gcc -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c
gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_kstring.o test/test_kstring.c
gcc -o test/test_kstring test/test_kstring.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_realn.o test/test_realn.c
gcc -o test/test_realn test/test_realn.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-regidx.o test/test-regidx.c
gcc -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_view.o test/test_view.c
gcc -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test_index.o test/test_index.c
gcc -o test/test_index test/test_index.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -g -Wall -O2 -I. -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -I. -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -o test/test-parse-reg test/test-parse-reg.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
rm -rf libgab/
git clone --recursive https://github.com/grenaud/libgab.git
Cloning into 'libgab'...
remote: Enumerating objects: 300, done.
remote: Total 300 (delta 0), reused 0 (delta 0), pack-reused 300
Receiving objects: 100% (300/300), 114.47 KiB | 626.00 KiB/s, done.
Resolving deltas: 100% (187/187), done.
make -C libgab
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c utils.cpp -o utils.o
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c testUtils.cpp -o testUtils.o
testUtils.cpp: In function ‘int main(int, char*)’:
testUtils.cpp:22:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
for(unsigned int c= 2147400000;c<10147400000;c+=1000000)
^~~
testUtils.cpp:24:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
return 0;
^~~~~~
make -C gzstream/
g++ -I. -O -c -o gzstream.o gzstream.C
ar cr libgzstream.a gzstream.o
g++ -o testUtils testUtils.o utils.o gzstream/libgzstream.a -lz
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c ReconsReferenceBAM.cpp -o ReconsReferenceBAM.o
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c PutProgramInHeader.cpp -o PutProgramInHeader.o
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c FastQObj.cpp -o FastQObj.o
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c FastQParser.cpp -o FastQParser.o
g++ -Wall -lm -O3 -I. -Igzstream/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/include/ -I/Users/bgppermp/Downloads/glactools-master/bamtools/build/src/include/ -c testRecons.cpp -o testRecons.o
g++ -o testRecons testRecons.o utils.o /Users/bgppermp/Downloads/glactools-master/bamtools/build/src/api/libbamtools.a ReconsReferenceBAM.o gzstream/libgzstream.a -lz
Undefined symbols for architecture x86_64:
"BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)", referenced from:
_main in testRecons.o
"BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char*&, unsigned int const&, unsigned int&) const", referenced from:
reconstructRefWithPosOnRead[abi:cxx11](BamTools::BamAlignment const*) in ReconsReferenceBAM.o
reconstructRefWithPos[abi:cxx11](BamTools::BamAlignment const*) in ReconsReferenceBAM.o
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::at(unsigned long) const", referenced from:
BamTools::Internal::SamHeaderValidator::CheckNameFormat(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamHeaderValidator_p.cpp.o)
BamTools::Internal::SamHeaderValidator::CheckSequencingTechnology(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamHeaderValidator_p.cpp.o)
BamTools::Internal::HttpRequestHeader::ParseLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, int) in libbamtools.a(HttpHeader_p.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::find(char, unsigned long) const", referenced from:
BamTools::Internal::SamHeaderValidator::ValidateVersion() in libbamtools.a(SamHeaderValidator_p.cpp.o)
BamTools::Internal::BamFtp::ParseUrl(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamFtp_p.cpp.o)
BamTools::Internal::BamFtp::ParsePassiveResponse() in libbamtools.a(BamFtp_p.cpp.o)
BamTools::Internal::BamHttp::ParseUrl(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamHttp_p.cpp.o)
BamTools::Internal::HttpHeader::ParseLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, int) in libbamtools.a(HttpHeader_p.cpp.o)
BamTools::Internal::HttpRequestHeader::ParseLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, int) in libbamtools.a(HttpHeader_p.cpp.o)
BamTools::Internal::HttpResponseHeader::ParseLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, int) in libbamtools.a(HttpHeader_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::rfind(char, unsigned long) const", referenced from:
BamTools::Internal::BamIndexFactory::CreateIndexFromFilename(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, BamTools::Internal::BamReaderPrivate*) in libbamtools.a(BamIndexFactory_p.cpp.o)
BamTools::Internal::BamIndexFactory::FileExtension(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamIndexFactory_p.cpp.o)
BamTools::Internal::HostAddress::ParseAddress() in libbamtools.a(HostAddress_p.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::compare(unsigned long, unsigned long, char const*, unsigned long) const", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamDeviceFactory::CreateDevice(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamDeviceFactory_p.cpp.o)
"std::__1::__vector_base_common::__throw_length_error() const", referenced from:
BamTools::BamAlignment::BamAlignment(BamTools::BamAlignment const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::BamAlignment::GetSoftClips(std::__1::vector<int, std::__1::allocator >&, std::__1::vector<int, std::__1::allocator >&, std::__1::vector<int, std::__1::allocator >&, bool) const in libbamtools.a(BamAlignment.cpp.o)
void std::__1::vector<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > > >::__push_back_slow_path<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const>(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::LoadNextAlignment(BamTools::BamAlignment&) in libbamtools.a(BamReader_p.cpp.o)
void std::__1::vector<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > > >::__push_back_slow_path<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const>(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamReader_p.cpp.o)
void std::__1::vector<BamTools::RefData, std::__1::allocatorBamTools::RefData >::__push_back_slow_path<BamTools::RefData const>(BamTools::RefData const&) in libbamtools.a(BamReader_p.cpp.o)
std::__1::vector<BamTools::CustomHeaderTag, std::__1::allocatorBamTools::CustomHeaderTag >::vector(std::__1::vector<BamTools::CustomHeaderTag, std::__1::allocatorBamTools::CustomHeaderTag > const&) in libbamtools.a(SamHeader.cpp.o)
...
"std::__1::__vector_base_common::__throw_out_of_range() const", referenced from:
BamTools::SamProgramChain::operator[](std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamProgramChain.cpp.o)
BamTools::SamSequenceDictionary::Remove(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamSequenceDictionary.cpp.o)
BamTools::SamSequenceDictionary::operator[](std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamSequenceDictionary.cpp.o)
BamTools::SamReadGroupDictionary::Remove(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamReadGroupDictionary.cpp.o)
BamTools::SamReadGroupDictionary::operator[](std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamReadGroupDictionary.cpp.o)
BamTools::Internal::BamToolsIndex::ReadReferenceEntry(BamTools::Internal::BtiReferenceEntry&) in libbamtools.a(BamToolsIndex_p.cpp.o)
BamTools::Internal::BamToolsIndex::HasAlignments(int const&) const in libbamtools.a(BamToolsIndex_p.cpp.o)
...
"std::__1::__basic_string_common::__throw_length_error() const", referenced from:
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, char) in libbamtools.a(BamAlignment.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::Close() in libbamtools.a(BamReader_p.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::GetNextAlignmentCore(BamTools::BamAlignment&) in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::LoadReferenceData() in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::Open(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamReader_p.cpp.o)
...
"std::__1::locale::use_facet(std::__1::locale::id&) const", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BgzfStream_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BamRandomAccessController_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >::operator<<(std::__1::basic_ostream<char, std::__1::char_traits >& ()(std::__1::basic_ostream<char, std::__1::char_traits >&)) in libbamtools.a(SamProgramChain.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const, unsigned long) in libbamtools.a(SamProgramChain.cpp.o)
BamTools::Internal::SamFormatParser::Parse(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
BamTools::Internal::BamStandardIndex::Create() in libbamtools.a(BamStandardIndex_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BamStandardIndex_p.cpp.o)
...
"std::__1::ios_base::getloc() const", referenced from:
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BgzfStream_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BamRandomAccessController_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >::operator<<(std::__1::basic_ostream<char, std::__1::char_traits >& ()(std::__1::basic_ostream<char, std::__1::char_traits >&)) in libbamtools.a(SamProgramChain.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const, unsigned long) in libbamtools.a(SamProgramChain.cpp.o)
BamTools::Internal::SamFormatParser::Parse(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
BamTools::Internal::BamStandardIndex::Create() in libbamtools.a(BamStandardIndex_p.cpp.o)
std::__1::basic_ostream<char, std::__1::char_traits >& std::__1::__put_character_sequence<char, std::__1::char_traits >(std::__1::basic_ostream<char, std::__1::char_traits >&, char const*, unsigned long) in libbamtools.a(BamStandardIndex_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::at(unsigned long)", referenced from:
BamTools::Internal::HttpResponseHeader::ParseLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, int) in libbamtools.a(HttpHeader_p.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::append(char const*, unsigned long)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamAlignment.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::Tag2Cigar(BamTools::BamAlignment&, BamTools::RaiiBuffer&) in libbamtools.a(BamReader_p.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, char const*) in libbamtools.a(BamReader_p.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BgzfStream_p.cpp.o)
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamRandomAccessController_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::append(unsigned long, char)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::assign(char const*)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
BamTools::SamHeader::SetHeaderText(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamHeader.cpp.o)
BamTools::Internal::BamToolsIndex::Create() in libbamtools.a(BamToolsIndex_p.cpp.o)
BamTools::Internal::BamToolsIndex::Jump(BamTools::BamRegion const&, bool*) in libbamtools.a(BamToolsIndex_p.cpp.o)
BamTools::Internal::BamToolsIndex::Load(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamToolsIndex_p.cpp.o)
BamTools::Internal::BamStandardIndex::Create() in libbamtools.a(BamStandardIndex_p.cpp.o)
BamTools::Internal::BamStandardIndex::Jump(BamTools::BamRegion const&, bool*) in libbamtools.a(BamStandardIndex_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::assign(char const*, unsigned long)", referenced from:
BamTools::BamAlignment::RemoveTag(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::LoadNextAlignment(BamTools::BamAlignment&) in libbamtools.a(BamReader_p.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::resize(unsigned long, char)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BgzfStream_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BamRandomAccessController_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(SamHeader.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(SamFormatParser_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::str(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BamStandardIndex_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::reserve(unsigned long)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::Tag2Cigar(BamTools::BamAlignment&, BamTools::RaiiBuffer&) in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamHttp::ParseUrl(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamHttp_p.cpp.o)
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::push_back(char)", referenced from:
std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > std::__1::operator+<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, char) in libbamtools.a(BamAlignment.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BgzfStream_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BamRandomAccessController_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(SamHeader.cpp.o)
std::__1::basic_istream<char, std::__1::char_traits >& std::__1::getline<char, std::__1::char_traits, std::__1::allocator >(std::__1::basic_istream<char, std::__1::char_traits >&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >&, char) in libbamtools.a(SamFormatParser_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(SamFormatParser_p.cpp.o)
std::__1::basic_stringbuf<char, std::__1::char_traits, std::__1::allocator >::overflow(int) in libbamtools.a(BamStandardIndex_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::basic_string(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&)", referenced from:
BamTools::BamAlignment::BamAlignment(BamTools::BamAlignment const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::BamAlignment::GetErrorString() const in libbamtools.a(BamAlignment.cpp.o)
BamTools::BamAlignment::GetTagNames() const in libbamtools.a(BamAlignment.cpp.o)
void std::__1::vector<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > > >::__push_back_slow_path<std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const>(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::Filename() const in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::GetErrorString() const in libbamtools.a(BamReader_p.cpp.o)
BamTools::Internal::BamReaderPrivate::GetReferenceID(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) const in libbamtools.a(BamReader_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::basic_string(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, unsigned long, unsigned long, std::__1::allocator const&)", referenced from:
BamTools::BamAlignment::BuildCharData() in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamIndexFactory::CreateIndexFromFilename(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, BamTools::Internal::BamReaderPrivate*) in libbamtools.a(BamIndexFactory_p.cpp.o)
BamTools::Internal::BamIndexFactory::FileExtension(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(BamIndexFactory_p.cpp.o)
BamTools::Internal::SamFormatParser::ParseSamLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
BamTools::Internal::SamFormatParser::ParseHDLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
BamTools::Internal::SamFormatParser::ParseSQLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
BamTools::Internal::SamFormatParser::ParseRGLine(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) in libbamtools.a(SamFormatParser_p.cpp.o)
...
"std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >::~basic_string()", referenced from:
BamTools::BamAlignment::SetErrorString(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&) const in libbamtools.a(BamAlignment.cpp.o)
BamTools::Internal::BamReaderPrivate::SetErrorString(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator

Hi,
I've been using glactools for a while now, with no issues, to manipulate files and export them to treemix format. Today I was working on a new sheep dataset and encountered a problem when setting the root:
glactools replaceanc SM_Sheep_Filtered.acf.gz M-0006.acf.gz > SM_Sheep_Filtered_root.acf.gz

error message: The reference allele differs between NC_019458.2 0 A,G 0,0:0 0,0:0 1,1:0 2,0:0 .... and NC_019458.2 0 G,A 1,1:0 1,1:0

Does anyone know what's the problem here and how can I solve it?

Thanks!

So, I just download glactools and I'm working through the pipeline to convert bam to plink (bam2acf, union, acf2bplink).

At union I'm getting this error. Why would this error be thrown?

glactools union ERR484729.acf ERR490277.acf > test2.acf

sanityCheck()1 Chromosomes differ between FLZR01000063.1 740 A,N 0,0:0 0,0:0 1,0:0 and FLZR01000063.1 740 A,N 0,0:0 0,0:0 1,0:0

Also, I know it's a FAQ, but I still don't understand the difference between a defined site (intersect) and undefined site (union), because I can get intersect to work without issues.

Thanks,
Mike

I got a error when I run it. I hope you can do me a favour.
I have two problem. first , when I run it in command line,my command is that:
glactools vcf2acf --fai Gmax_275_v2.0.fa.fai --onlyGT Z-001.recode.vcf Z-001 > a.acf.gz
but I got a warning like that :
Warning: if several sites are rejected due to being empty, it could be due to the absence of the PL field, please rerun using the onlyGT flag.
Program terminated gracefully.
I have already used the onlyGT flag. I don't know why and here is my vcf file:
##fileformat=VCFv4.2
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Z-001
1 4485 Chr01_4485 G A . . . GT 1/1
1 5564 Chr01_5564 C T . . . GT 0/0
1 5698 Chr01_5698 C T . . . GT 0/0
1 5899 Chr01_5899 T C . . . GT 1/1
the seconded problem. when I run it in a script , It don't have a result. my script is like that:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -S /bin/bash

#$ -l mem_free=4G

VCFTOOLS=/share/apps/vcftools/vcftools-0.1.15
GLACTOOLS=/ds3512/home/panyp/ruanjian/glactools/
SAMTOOLS=/ds3512/home/panyp/ruanjian/samtools-1.9/bin
DIR=/ds3512/home/panyp/diff_genome/
$SAMTOOLS/samtools faidx $DIR/Gmax_275_v2.0.fa
$VCFTOOLS --vcf chr01.recode.vcf --indv Z-001 --out Z-001 --recode
$GLACTOOLS/glactools vcf2acf --fai $DIR/Gmax_275_v2.0.fa.fai --onlyGT Z-001.recode.vcf Z-001 > Z-001.acf.gz
Z-001 is my sample ID. It generate a 'Z-001.acf.gz' file but the file can't be decompressed :
gzip: Z-001.acf.gz: unexpected end of file.
I check the log and find that:
Filter used: Cutoffs :
Minimum genotype quality (GQ) = 0
Minimum RMS of the mapping qualities (MQ) = 0
Minimum mapability = 0
Filter sites close to an indel = currently turned on/used
Filter sites close labeled as repeat masked (RM) = currently turned on/used
Filter sites close labeled as systematic error (SysErr) = currently turned on/used
Minimum coverage = 0
Minimum coverage = 1000
Cannot write to /dev/stdout.

Hello,

Thank you for a very useful program.
I have been trying to generated a GROSS input file using glactools and the following tutorial: https://github.com/FerRacimo/GRoSS/blob/master/VCFtoGRoSS.md

I have tried the following command:
glactools vcfm2acf --onlyGT --fai ref.fasta.fai input.vcf - |glactools meld -f panel3.txt - | glactools acf2gross --noroot - |gzip > output.gross.gz

And I received the following error messages:
Error: GlacParser tried to read 4 bytes but got 0
Error: GlacParser tried to read 4 bytes but got 0

I have also tried this and received the same errors messages:
tabix -h input.vcf |glactools vcfm2acf --onlyGT --fai ref.fasta.fai - |glactools meld -f panel3.txt - | glactools acf2gross --noroot - |gzip > output.gross.gz

I've tried the following command to convert the vcf file to an acf file and it worked fine.
glactools vcfm2acf --onlyGT --fai ref.fasta.fai input.vcf > output.acf.gz

The file looks as follow:
glactools view -h check.acf.gz|head
Warning: No EOF marker, likely due to an I/O error #chr coord REF,ALT root anc SP1060 KW IR23 IR24 IR30 IR33 IR34 IR36 S10 S12 S27 S31 S37 S38 S39 S40 S41 S42 S43 S53 S54 S56 14Tt001 14Tt004 14Tt006 14Tt021 14Tt022 14Tt023 14Tt025 7Tt156 7Tt161 7Tt182 7Tt193 7Tt270 7Tt278 7Tt282 7Tt284 7Tt287 7Tt350 MRVK01001050.1 1309 G,A 0,0:0 0,0:0 0,0:0 2,0:0 0,2:0 0,2:0 1,1:0 2,0:0 2,0:0 2,0:0 2,0:0 1,1:0 1,1:0 2,0:0 1,1:0 2,0:0 2,0:0 1,1:0 2,0:0 2,0:0 0,0:0 2,0:0 1,1:0 2,0:0 2,0:0 0,0:0 2,0:0 2,0:0 2,0:0 2,0:0 2,0:0 0,0:0 2,0:0 0,0:0 0,2:0 1,1:0 2,0:0 2,0:0 2,0:0 1,1:0 2,0:0

The vcf file is as follow for the same SNP:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SP1060 KW IR23 IR24 IR30 IR33 IR34 IR36 S10 S12 S27 S31 S37 S38 S39 S40 S41 S42 S43 S53 S54 S56 14Tt001 14Tt004 14Tt006 14Tt021 14Tt022 14Tt023 14Tt025 7Tt156 7Tt161 7Tt182 7Tt193 7Tt270 7Tt278 7Tt282 7Tt284 7Tt287 7Tt350MRVK01001050.1 1309 . G A 999 . DP=803;VDB=0.353011;SGB=99.994;RPB=0.358603;MQB=1;MQSB=1;BQB=0.917396;MQ0F=0;ICB=0.411676;HOB=0.0799516;AC=14;AN=68;DP4=299,323,78,72;MQ=60 GT:PL:DP:GP:GQ ./.:0,0,0:0:0,0,0:0 0/0:0,27,242:9:0,30,254:30 1/1:255,54,0:18:242,44,0:44 1/1:255,33,0:11:242,23,0:23 0/1:105,0,224:11:101,0,233:99 0/0:0,54,255:18:0,57,267:57 0/0:0,36,255:12:0,39,267:39 0/0:0,57,255:19:0,60,267:60 0/0:0,69,255:23:0,72,267:72 0/1:194,0,201:15:190,0,210:99 0/1:196,0,255:18:192,0,264:99 0/0:0,33,255:11:0,36,267:36 0/1:50,0,178:8:46,0,187:46 0/0:0,48,255:16:0,51,267:51 0/0:0,33,255:11:0,36,267:36 0/1:233,0,255:19:229,0,264:99 0/0:0,48,255:16:0,51,267:51 0/0:0,36,255:12:0,39,267:39 ./.:229,27,0:9:216,17,0:17 0/0:0,42,255:14:0,45,267:45 0/1:121,0,175:11:117,0,184:99 0/0:0,54,255:18:0,57,267:57 0/0:0,48,255:16:0,51,267:51 ./.:0,9,255:23:0,12,267:12 0/0:0,45,255:15:0,48,267:48 0/0:0,42,255:14:0,45,267:45 0/0:0,51,255:17:0,54,267:54 0/0:0,45,255:15:0,48,267:48 0/0:0,60,255:20:0,63,267:63 ./.:255,20,0:14:242,11,0:11 0/0:0,36,237:12:0,39,249:39 ./.:241,0,8:11:237,0,17:17 1/1:255,39,0:13:242,29,0:29 0/1:163,0,207:14:159,0,216:99 0/0:0,51,255:17:0,54,267:54 0/0:0,33,255:11:0,36,267:36 0/0:0,66,255:22:0,69,267:69 0/1:242,0,178:16:238,0,187:990/0:0,33,255:11:0,36,267:36

The first sample is ancient and has more missing genotype than the others.

Could you please help?
Thank you very much,

Marie

I've come across an issue when trying to convert .acf to .beta for use with BetaScan.

I can generate acf files using the command:
glactools vcfm2acf --onlyGT --fai ref.fai pops.chr9.vcf > pops.chr9.acf

and the format looks fine, e.g.

#chr    coord   REF,ALT   root       anc     pop1    pop2    pop3    pop4
9       5895    G,T       0,0:0      0,0:0   49,60:0 0,0:0   0,0:0   0,0:0
9       5929    A,G       0,0:0      0,0:0   0,0:0   14,16:0 0,0:0   0,0:0
9       5979    T,G       1,26:0    1,26:0   0,0:0   0,0:0   0,0:0   77,5:0

where each population was extracted from a multi sample vcf with the vcftools flag --mac 1. I then merged the samples into the populations and set the root and anc as detailed in the README.

Converting from acf to beta:
glactools acf2betascan --useroot pops.rooted.chr9.acf.gz | gzip > pops.rooted.chr9.beta.txt.gz

is when I receive the error for the majority of positions:
Cannot determine the root allele for 9 5979 T,G 1,26:0 1,26:0 0,0:0 0,0:0 0,0:0 77,5:0

But then it reports:
Program ACF2BETASCAN looked at 1227 records, terminated gracefully

Yet the resulting beta.txt files are empty. Any ideas please?

Cheers

Cooper

Hi,
I used glactools to convert multiple sample vcf file to acf format. However, a problem has occured as follows:

(base) [shali@vm-login02 test]$ glactools vcfm2acf --onlyGT --fai /public/home/fan_lab/shali/reference/hg38.fa.fai chr22.vcf.gz > chr22.acf.gz
SimpleVCF: cannot observed both GL and PL

My vcf file was generated by PEPPER-Margin-DeepVariant pipeline, regenotyped by whatshap and filtered by vcftools. Two lines of this file are shown below, and I think it do contains GL at least:

chr22   10510059        .       G       C       .       PASS    .       GT:GQ:DP:AD:VAF:PL:GL   0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     0/0:9:.:.:.:.:-0.0536517,-0.93475,-9.23491      0/0:13:.:.:.:.:-0.0234915,-1.27857,-13.7954     0/0:9:.:.:.:.:-0.0536517,-0.93475,-9.23491      0/0:36:.:.:.:.:-0.000114312,-3.57975,-9.18137   .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       0/1:6:.:.:.:.:-0.560206,-0.139841,-5.15084      0/0:42:.:.:.:.:-2.9343e-05,-4.17029,-13.7719    .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       0/0:42:.:.:.:.:-2.9343e-05,-4.17029,-13.7719    .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       0/0:36:.:.:.:.:-0.000114312,-3.57975,-9.18137   1/1:7:.:.:.:.:-4.68986,-0.689859,-0.0992291     0/0:9:.:.:.:.:-0.0536517,-0.93475,-9.23491      .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     0/0:9:.:.:.:.:-0.0536044,-0.93511,-9.23486
chr22   10510248        .       G       A       .       PASS    .       GT:GQ:DP:AD:VAF:PL:GL   0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     0/0:42:.:.:.:.:-2.9343e-05,-4.17029,-13.7719    0/0:13:.:.:.:.:-0.0234915,-1.27857,-13.7954     0/0:9:.:.:.:.:-0.0536517,-0.93475,-9.23491      0/0:42:.:.:.:.:-2.9343e-05,-4.17029,-13.7719    .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       0/0:42:.:.:.:.:-2.9343e-05,-4.17029,-13.7719    0/1:4:.:.:.:.:-0.370817,-0.24092,-9.55208       0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     0/0:45:.:.:.:.:-1.50329e-05,-4.46075,-18.3625   .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       0/0:42:.:.:.:.:-2.9343e-05,-4.17029,-13.7719    0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     0/0:9:.:.:.:.:-0.0536517,-0.93475,-9.23491      .:.:.:.:.:.:-0.477121,-0.477121,-0.477121       1/1:7:.:.:.:.:-4.68986,-0.689859,-0.0992291     0/0:7:.:.:.:.:-0.0992
291,-0.689859,-4.68986     0/0:7:.:.:.:.:-0.0992291,-0.689859,-4.68986     0/0:9:.:.:.:.:-0.0536044,-0.93511,-9.23486

May I have some help from anybody? Thanks!

I am on Ubuntu 16.04. Late in make, I get the following errors:

/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:171: undefined reference to curl_easy_getinfo' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:185: undefined reference to curl_easy_getinfo'
htslib/libhts.a(hfile_libcurl.o): In function wait_perform': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:693: undefined reference to curl_multi_fdset'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:714: undefined reference to curl_multi_perform' htslib/libhts.a(hfile_libcurl.o): In function process_messages':
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:669: undefined reference to curl_multi_info_read' htslib/libhts.a(hfile_libcurl.o): In function wait_perform':
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:696: undefined reference to curl_multi_timeout' htslib/libhts.a(hfile_libcurl.o): In function libcurl_close':
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1073: undefined reference to curl_easy_pause' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1082: undefined reference to curl_multi_remove_handle'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1086: undefined reference to curl_easy_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1087: undefined reference to curl_multi_cleanup'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1082: undefined reference to curl_multi_remove_handle' htslib/libhts.a(hfile_libcurl.o): In function libcurl_write':
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:845: undefined reference to curl_easy_pause' htslib/libhts.a(hfile_libcurl.o): In function libcurl_exit':
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:274: undefined reference to curl_share_cleanup' htslib/libhts.a(hfile_libcurl.o): In function restart_from_position':
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:950: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:969: undefined reference to curl_easy_duphandle'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:973: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:974: undefined reference to curl_easy_setopt'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:975: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1052: undefined reference to curl_easy_cleanup'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:985: undefined reference to curl_multi_add_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1052: undefined reference to curl_easy_cleanup'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1052: undefined reference to curl_easy_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:992: undefined reference to curl_easy_pause'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1012: undefined reference to curl_multi_remove_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1015: undefined reference to curl_easy_reset'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1016: undefined reference to curl_multi_remove_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1044: undefined reference to curl_easy_reset'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1045: undefined reference to curl_multi_remove_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1025: undefined reference to curl_easy_cleanup'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1027: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1028: undefined reference to curl_easy_setopt'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1018: undefined reference to curl_easy_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1031: undefined reference to curl_easy_reset'
htslib/libhts.a(hfile_libcurl.o): In function libcurl_open': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1148: undefined reference to curl_multi_init'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1151: undefined reference to curl_easy_init' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1155: undefined reference to curl_easy_setopt'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1159: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1167: undefined reference to curl_easy_setopt'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1168: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1169: undefined reference to curl_easy_setopt'
htslib/libhts.a(hfile_libcurl.o):/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1176: more undefined references to curl_easy_setopt' follow htslib/libhts.a(hfile_libcurl.o): In function libcurl_open':
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1207: undefined reference to curl_multi_add_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1215: undefined reference to curl_easy_getinfo'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1235: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1236: undefined reference to curl_easy_setopt'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1237: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1248: undefined reference to curl_easy_getinfo'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1258: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1259: undefined reference to curl_easy_setopt'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1286: undefined reference to curl_easy_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1287: undefined reference to curl_multi_cleanup'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1279: undefined reference to curl_multi_remove_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1162: undefined reference to curl_easy_setopt'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1163: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1202: undefined reference to curl_easy_setopt'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1194: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1269: undefined reference to curl_easy_getinfo'
htslib/libhts.a(hfile_libcurl.o): In function libcurl_read': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:786: undefined reference to curl_easy_pause'
htslib/libhts.a(hfile_libcurl.o): In function hfile_plugin_init_libcurl': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1447: undefined reference to curl_global_init'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1450: undefined reference to curl_share_init' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1452: undefined reference to curl_share_setopt'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1453: undefined reference to curl_share_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1454: undefined reference to curl_share_setopt'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1480: undefined reference to curl_version_info' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1456: undefined reference to curl_share_cleanup'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1457: undefined reference to curl_global_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1469: undefined reference to curl_share_cleanup'
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1470: undefined reference to curl_global_cleanup' htslib/libhts.a(hfile_libcurl.o): In function libcurl_exit':
/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:296: undefined reference to `curl_global_cleanup'
collect2: error: ld returned 1 exit status
Makefile:54: recipe for target 'glactools' failed
make: *** [glactools] Error 1
glactools$

And I have:
glactools$ curl --version
curl 7.47.0 (x86_64-pc-linux-gnu) libcurl/7.47.0 GnuTLS/3.4.10 zlib/1.2.8 libidn/1.32 librtmp/2.3
Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3 pop3s rtmp rtsp smb smbs smtp smtps telnet tftp
Features: AsynchDNS IDN IPv6 Largefile GSS-API Kerberos SPNEGO NTLM NTLM_WB SSL libz TLS-SRP UnixSockets

Have I missed something?

hello, grenaud! now, I just have an outgroup vcf file (other mammals not human), could you tell me how can I transform vcf file to epo file?

Hi Grenaud,

I've never had any problem with the glactools acf2betascan conversion before, until today when it is outputting fewer loci than are input.

glactools acf2betascan --fold qt6.acf > qt6.beta.txt
Program ACF2BETASCAN looked at 9005 records, terminated gracefully

9005 is the correct number of SNP loci. But...

wc qt6.beta.txt
8961 26883 106058 qt6.beta.txt

Can you help me find where my missing 44 loci went and how to get them back?

Hello.

I have a problem using vcfm2acf.

glactools vcfm2acf --onlyGT --fai 1-12.fai sorted.output.vcf

error message:
SimpleVCF: for line -18.3084 0 -12.4722 -19.8136 -14.5794 -34.0463 -19.8136 -14.5794 -34.0463 -34.0463 -19.8136 -14.5794 -34.0463 -34.0463 -34.0463 the GL field does not have 3 or 6 fields

The VCF file is form Freebayes, filtered with vbcftools.

Thanks.

Heng

hello, i want to install this software,but i meet this question as follows,please help me to solved its.

bam_ampliconclip.c: In function ‘amplicon_clip_main’:
bam_ampliconclip.c:639:23: warning: ‘sites’ may be used uninitialized in this function [-Wmaybe-uninitialized]
bed_entry_list_t *sites;
^
gcc -g -Wall -O2 -I. -I../htslib -I./lz4 -c -o amplicon_stats.o amplicon_stats.c
gcc -g -Wall -O2 -I. -I../htslib -I./lz4 -c -o bam_import.o bam_import.c
bam_import.c: In function ‘import_fastq’:
bam_import.c:180:35: error: ‘FASTQ_OPT_NAME2’ undeclared (first use in this function)
hts_set_opt(fp_in[i], FASTQ_OPT_NAME2, 1);
^
bam_import.c:180:35: note: each undeclared identifier is reported only once for each function it appears in
make[1]: *** [Makefile:138: bam_import.o] Error 1
make[1]: Leaving directory '/home/pengyan/biosoft/glactools-master/samtools'
make: *** [Makefile:47: samtools/libbam.a] Error 2

Hi Gabriel,

I'm wanted to test out some different PL options in the glf2acf conversion, but I am getting an error.

The default option works great, with a command like this:
glactools glf2acf file.glf.gz > file.default_PL.acf.gz

But when I add a PL option to the same command:
glactools glf2acf --minPL 30 file.glf.gz > file.30_PL.acf.gz

I get this error message:
The last argument is the <glf file>

I also tried the -u option for uncompressed output and it gives the same error message. Could you please let me know if options should be entered differently or if there is a bug to fix?

Thanks!
Nathan

Hi, grenaud, I met a problem when compile the glactools,Can you give me some advise ? Thank you very.

g++ -std=c++11 -Wall -lm -O3 -lz -Ihtslib/ -Ibamtools/include/ -Ibamtools/src/ -Itabixpp/ -I/ds3512/home/panyp/ruanjian/glactools-1.0.5/libgab -I/ds3512/home/panyp/ruanjian/glactools-1.0.5/libgab/gzstream/ -c glactools.cpp -o glactools.o
In file included from GlacParser.h:17,
from BAM2ACF.h:31,
from glactools.cpp:13:
htslib/hts_internal.h:126:68: error: expected primary-expression before 'static'
static inline int find_file_extension(const char *fn, char ext_out[static HTS_MAX_EXT_LEN])
^~~~~~
htslib/hts_internal.h:126:68: error: expected ']' before 'static'
static inline int find_file_extension(const char *fn, char ext_out[static HTS_MAX_EXT_LEN])
^~~~~~
]
htslib/hts_internal.h:126:68: error: expected ')' before 'static'
static inline int find_file_extension(const char *fn, char ext_out[static HTS_MAX_EXT_LEN])
~ ^~~~~~
)
htslib/hts_internal.h:126:68: error: expected initializer before 'static'
static inline int find_file_extension(const char *fn, char ext_out[static HTS_MAX_EXT_LEN])
^~~~~~
In file included from BAM2ACF.h:31,
from glactools.cpp:13:
GlacParser.h:30:13: warning: 'sizeBytesGLF' defined but not used [-Wunused-variable]
static char sizeBytesGLF;
^~~~~~~~~~~~
GlacParser.h:29:13: warning: 'sizeBytesACF' defined but not used [-Wunused-variable]
static char sizeBytesACF;
^~~~~~~~~~~~
GlacParser.h:27:16: warning: 'maskAlt' defined but not used [-Wunused-variable]
static uint8_t maskAlt=15; //00001111
^~~~~~~
GlacParser.h:25:16: warning: 'maskRef' defined but not used [-Wunused-variable]
static uint8_t maskRef=240; //11110000
^~~~~~~
make: *** [glactools.o] Error 1

Hi,

I am attempting to compile your package from github however, I am receiving the following error messages (below). Do you know the meaning of these or how to rectify the problem? Any help would be much appreciated.

Thank you and best wishes,

Dean

.../glactools/tabixpp/htslib/cram/cram_codecs.c:1768: undefined reference to __intel_sse2_strlen' htslib/libhts.a(cram_codecs.o): In function cram_byte_array_stop_decode_block':
.../glactools/tabixpp/htslib/cram/cram_codecs.c:1682: undefined reference to _intel_fast_memcpy' collect2: error: ld returned 1 exit status make[2]: *** [tabix++] Error 1 make[2]: Leaving directory .../glactools/tabixpp'
make[1]: *** [all-recur] Error 1
make[1]: Leaving directory `.../glactools/tabixpp'
make: *** [tabixpp/tabix.o] Error 2

Hi
I Need Convert plink(bed-bim-fam) to treemix input
With This Command:
glactools bplink2acf --fai human_g1k_v37.fasta.fai afghan | glactools acf2treemix - | gzip > treemix.gz

but error:

Cannot write to /dev/stdout
Error: GlacParser tried to read 4 bytes but got 0

Data:
https://evolbio.ut.ee/afghan/

Hi, I have a multi-samples VCF that I would like to convert to G-Phocs input format.
Is there a way to accomplish this task in glactools?
Thank you!

hi,when I installed glactools,I met a problem like that,can you give me some advise. Thank you very much.

ReadTabix.cpp:(.text+0x1a8): undefined reference to Tabix::setRegion(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)' lib/libglactools.a(ReadTabix.o): In function ReadTabix::readLine(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)':
ReadTabix.cpp:(.text+0x20d): undefined reference to Tabix::getNextLine(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)' lib/libglactools.a(ReadTabix.o): In function ReadTabix::ReadTabix(std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int, int)':
ReadTabix.cpp:(.text+0x344): undefined reference to Tabix::Tabix(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)' ReadTabix.cpp:(.text+0x60a): undefined reference to Tabix::setRegion(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)'
lib/libglactools.a(ReadTabix.o): In function ReadTabix::repositionIterator(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int)': ReadTabix.cpp:(.text+0xafb): undefined reference to Tabix::setRegion(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)'
collect2: error: ld returned 1 exit status
make: *** [glactools] Error 1