compile errors

[shiyi-pan]

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

[grenaud]

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

[shiyi-pan]

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:

##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.

[grenaud]

great! Would you mind that we close this issue and could you open a new one?

[shiyi-pan]

thank you,you can close this one .