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annotate-output(1) [centos man page]

ANNOTATE-OUTPUT(1)					      General Commands Manual						ANNOTATE-OUTPUT(1)

NAME
annotate-output - annotate program output with time and stream SYNOPSIS
annotate-output [options] program [args ...] DESCRIPTION
annotate-output will execute the specified program, while prepending every line with the current time and O for stdout and E for stderr. OPTIONS
+FORMAT Controls the timestamp format, as per date(1). Defaults to "%H:%M:%S". -h, --help Display a help message and exit successfully. EXAMPLE
$ annotate-output make 21:41:21 I: Started make 21:41:21 O: gcc -Wall program.c 21:43:18 E: program.c: Couldn't compile, and took me ages to find out 21:43:19 E: collect2: ld returned 1 exit status 21:43:19 E: make: *** [all] Error 1 21:43:19 I: Finished with exitcode 2 BUGS
Since stdout and stderr are processed in parallel, it can happen that some lines received on stdout will show up before later-printed stderr lines (and vice-versa). This is unfortunately very hard to fix with the current annotation strategy. A fix would involve switching to PTRACE'ing the process. Giving nice a (much) higher priority over the executed program could however cause this behaviour to show up less frequently. The program does not work as well when the output is not linewise. In particular, when an interactive program asks for input, the question might not be shown until after you have answered it. This will give the impression that the annotated program has hung, while it has not. SEE ALSO
date(1) SUPPORT
This program is community-supported (meaning: you'll need to fix it yourself). Patches are however appreciated, as is any feedback (posi- tive or negative). AUTHOR
annotate-output was written by Jeroen van Wolffelaar <jeroen@wolffelaar.nl> This manpage comes under the same copyright as annotate-output itself, read /usr/bin/annotate-output (or wherever you install it) for the details. DEBIAN
Debian Utilities ANNOTATE-OUTPUT(1)

Check Out this Related Man Page

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)
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