Closed shiyi-pan closed 4 years ago
Dear shiyi-pan, just to check do you have the latest version? The "hts_internal" problem was fixed a few days ago. Could you run the following:
make clean
git status
git pull origin master
make
Could you paste the contents of: .git/logs/HEAD
thank you ,grenaud . I downloaded the latest version and compiled the software. But I got a new 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:
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:
#
#
# 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/
$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:
Cannot write to /dev/stdout.
great! Would you mind that we close this issue and could you open a new one?
thank you,you can close this one .
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