You can compile and link using compiler options. The library is referenced using -l<its_name_here> and the path to the library using -L/path/to/lib.
-I is for the path to include directories.
However, if the library isn't in a directory in the linkers path when you run the executable you'll get an error. One way to solve this is to use rpath option.
someting like:
Note: I'm guessing what you need and what each item is. -I should be used with the path to header -l prepended to the library name and -L preceding the path to the library.
I have created symbolic links to several frequently used commands, for example:
"lt" is a link to "ls -ltrgo|tail". What can I do to make these links available system-wide, or at least in the directories my coworkers are in most of the time? I have copied the link to several directories, and... (6 Replies)
Hi, I have a task to search for a file called 'Xstartup' in the whole system because there might be different versions of it which overrite eachother.
Can anyone suggest a smart command to run this search ? The machine needs to scan every single folder beginning from root.
Please help, I am... (5 Replies)
Yea i was wondering how i would mount, and create a FAT directory that way i can save files in the FAT directory in a windows system and be able to access them on Linux systems. Or if there is any other way to share files between Linux and Windows. Any responds will help... thanks! (2 Replies)
Hello,
I am new to shell scripting and I was trying to write a script that would force a system wide password change except for admins. I am having some trouble and any help that someone could give me would be greatly appreciated. I am trying to do it by using the UID as the marker for anyone... (6 Replies)
Hi,
I need to look for a config file (ldap.conf) and pick the latest modified file.
`locate` tells me there are many ldap.conf's, some in /etc, /usr, /home, etc.
Is there some way I can sort them by last modified time via bash?
I was thinking maybe I could pipe the output of `locate` to `ls... (4 Replies)
I have installed user-mode linux kernel in Ubuntu 10.10 with the help of Synaptic package manager.
But I'm not getting how to run it.
If we install it manually, we've to run it using the executable binary file.
But here, I'm unable to locate any such file.
Please help....
Thanking You....
... (0 Replies)
When looking for wherever a program or a filename appears in the system, a short scrip is "findinner" which another script calls with a long parameter list consisting of path names ending with ".sh" or ".menu". "findinner" looks like this:
# If not .savenn file, show name and result of grep.
#... (4 Replies)
Discussion started by: wbport
4 Replies
LEARN ABOUT DEBIAN
vcf-annotate
VCF-ANNOTATE(1) User Commands VCF-ANNOTATE(1)NAME
vcf-annotate - annotate VCF file, add filters or custom annotations
SYNOPSIS
cat in.vcf | vcf-annotate [OPTIONS] > out.vcf
DESCRIPTION
About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.
Currently annotates only the INFO column, but it will be extended on demand.
OPTIONS -a, --annotations <file.gz>
The tabix indexed file with the annotations: CHR FROM[ TO][ VALUE]+.
-c, --columns <list>
The list of columns in the annotation file, e.g. CHROM,FROM,TO,-,INFO/STR,INFO/GN. The dash in this example indicates that the third
column should be ignored. If TO is not present, it is assumed that TO equals to FROM.
-d, --description <file|string>
Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'. The descriptions can be read from a
file, one annotation per line.
-f, --filter <list>
Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.
-h, -?, --help
This help message.
Filters:
+ Apply all filters with default values (can be overridden, see the example below).
-X Exclude the filter X
1, StrandBias
FLOAT Min P-value for strand bias (given PV4) [0.0001]
2, BaseQualBias
FLOAT Min P-value for baseQ bias [1e-100]
3, MapQualBias
FLOAT Min P-value for mapQ bias [0]
4, EndDistBias
FLOAT Min P-value for end distance bias [0.0001]
a, MinAB
INT Minimum number of alternate bases [2]
c, SnpCluster
INT1,INT2 Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases []
D, MaxDP
INT Maximum read depth [10000000]
d, MinDP
INT Minimum read depth [2]
q, MinMQ
INT Minimum RMS mapping quality for SNPs [10]
Q, Qual
INT Minimum value of the QUAL field [10]
r, RefN
Reference base is N []
W, GapWin
INT Window size for filtering adjacent gaps [10]
w, SnpGap
INT SNP within INT bp around a gap to be filtered [10]
Example:
zcat in.vcf.gz | vcf-annotate -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz zcat in.vcf.gz | vcf-annotate -f
+/-a/c=3,10/q=3/d=5/-D -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz
Where descriptions.txt contains:
key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name' key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'
vcf-annotate 0.1.5 July 2011 VCF-ANNOTATE(1)