...
and the respective lsof output (before and after (but before file closing) the mv operation) :
Even though attributed "deleted", the file's contents is still available and readable. Of course, once unlinked, the file can't be reopened / reused in its original location.
Hi @RudiC
I'm embarrassed to ask how can I repeat this conclusion. Broke all my spears
Can't beat these elusive moments of time.
Thanks
I am on a HP-UX machine I have a directory called "/u01/blobs" and the files look like this:
ls -1
7398
7399
7400
I need to produce a comma delimited file with the following format:
filename,location/filename
i.e:
7398,/u01/blobs/7398
7399,/u01/blobs/7399
7400,/u01/blobs/7400
What... (3 Replies)
Hello guys, thank God that I found this forum.
I hope that someone can help me because I don't have any idea on how to start it. I know that for some of you this is a very simple task but I'm not as advance on shell scripting like many people out there.
I got this file with a permanent... (10 Replies)
Hello all.
I am new to this forum (and somewhat new to UNIX / LINUX - I started using ubuntu 1 year ago).:b:
I have the following problem that I have not been able to figure out how to take care of and I was wondering if anyone could help me out.:confused:
I have all of my music stored in... (7 Replies)
Hi guys, I am a newbie here :wall:
I need a script that can search for a file in a directory and copy the contents of that file in a new file.
Please help me. :confused: Thanks in advance~ (6 Replies)
I hope some one can help me
I have multiple files in a directory with out extension like as below mentioned. But i want to change all the file names along .DDMMYYYYHHMISS format. And all files should have same DDMMYYYYHHMISS.
Scenario:
direcory name = /vol/best/srcfiles
files in a... (4 Replies)
I have to write a script to rename the every last sub-directory in a directory structure if the last sub-directory name doesn't contain "submitted".
eg:
given directory path:/u01/home/somedir
somedir can have many subdirectories and each subdirectory inturn has many subdirectories.
somedir... (3 Replies)
Hello All,
Can you help me in writing a script for reading the specific position data in a file and if that data found in that file that particular file should be renamed.
Ex: Folder : C:\\test
and Filename : CLSACK_112214.txt,CLSACK_112314.txt,CLSACK_112414.txt
Contents in the file would... (3 Replies)
I am trying to use the two files shown below to either remove or rename contents in one of those files. If in file1.txt $5 matches $5 of file2.txt and the value in $1 of file1.txt is not "No Match" then that value is substituted for all values in $5 and $1 of file2.txt. If however in $1 ... (5 Replies)
I have a specific set (all ending with .bam) of downloaded files in a directory /home/cmccabe/Desktop/NGS/API/2-15-2016. What I am trying to do is use a match to $2 in name to rename the downloaded files. To make things a more involved the date of the folder is unique and in the header of name... (1 Reply)
Hi All,
Just started learning unix and stuck into below issue.
Suppose i have folder structure as below.
Dir1/Dir2/Dir3/File1.msg
I am looking to rename the file name from File1.msg to File2.msg but from the parent Dir1
From Dir3 i can easily run the command like
mv File1.msg... (2 Replies)
Discussion started by: Gurjeet Singh
2 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)