The awk is close but hopefully the below explanation helps. Both file1 and file2 are tab-delineated, since $1 and $2 of file1 match $1 and $2 in file2, the last 4 strings in file2 are copied to the end of the matching file1 line. In thiscase the last 4 strings are GOOD 399 reads hom and are in bold in file2. Thank you very much .
file1
Code:
Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene PopFreqMax CLINSIG CLNDBN CLNACC CLNDSDB CLNDSDBID common
chr1 949654 949654 A G exonic ISG15 . synonymous SNV ISG15:NM_005101:exon2:c.294A>G:p.V98V 0.96 . . . . . .
file2
Code:
##.....
##.....
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NS12911_BC1
chr1 949654 . A G 3825.28 PASS AF=1;AO=621;DP=624;FAO=399;FDP=399;FR=.;FRO=0;FSAF=225;FSAR=174;FSRF=0;FSRR=0;FWDB=0.00425236;FXX=0.00249994;HRUN=1;LEN=1;MLLD=97.922;OALT=G;OID=.;OMAPALT=G;OPOS=949654;OREF=A;PB=0.5;PBP=1;QD=38.3487;RBI=0.0367904;REFB=0.0353003;REVB=-0.0365438;RO=2;SAF=335;SAR=286;SRF=0;SRR=2;SSEN=0;SSEP=0;SSSB=0.00332809;STB=0.5;STBP=1;TYPE=snp;VARB=-3.42335e-05;ANN=ISG15 GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR 1/1:171:624:399:2:0:621:399:1:286:335:0:2:174:225:0:0 GOOD 399 reads hom
desired output
Code:
Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene PopFreqMax CLINSIG CLNDBN CLNACC CLNDSDB CLNDSDBID common
chr1 949654 949654 A G exonic ISG15 . synonymous SNV ISG15:NM_005101:exon2:c.294A>G:p.V98V 0.96 . . . . . . GOOD 399 reads hom
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file
12
123 FP
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awk
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desired output
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Discussion started by: cmccabe
6 Replies
LEARN ABOUT DEBIAN
h5diff
h5diff(1) General Commands Manual h5diff(1)NAME
h5diff - Compares two HDF5 files and reports the differences.
SYNOPSIS
h5diff file1 file2 [OPTIONS] [object1 [object2 ] ]
DESCRIPTION
h5diff is a command line tool that compares two HDF5 files, file1 and file2, and reports the differences between them.
Optionally, h5diff will compare two objects within these files. If only one object, object1, is specified, h5diff will compare object1 in
file1 with object1 in file2. In two objects, object1 and object2, are specified, h5diff will compare object1 in file1 with object2 in
file2. These objects must be HDF5 datasets.
object1 and object2 must be expressed as absolute paths from the respective file's root group.
Additional information, with several sample cases, can be found in the document H5diff Examples.
OPTIONS
file1 file2
The HDF5 files to be compared.
-h Print all differences.
-r Print only the names of objects that differ; do not print the differences. These objects may be HDF5 datasets, groups, or named
datatypes.
-n count
Print difference up to count differences, then stop. count must be a positive integer.
-d delta
Print only differences that are greater than the limit delta. delta must be a positive number. The comparison criterion is whether
the absolute value of the difference of two corresponding values is greater than delta (e.g., |a-b| > delta, where a is a value in
file1 and b is a value in file2).
-p relative
Print only differences that are greater than a relative error. relative must be a positive number. The comparison criterion is
whether the absolute value of the difference 1 and the ratio of two corresponding values is greater than relative (e.g., |1-(b/a)| >
relative where a is a value in file1 and b is a value in file2).
object1 object2
Specific object(s) within the files to be compared.
EXAMPLES
The following h5diff call compares the object /a/b in file1 with the object /a/c in file2:
h5diff file1 file2 /a/b /a/c
This h5diff call compares the object /a/b in file1 with the same object in file2:
h5diff file1 file2 /a/b
And this h5diff call compares all objects in both files:
h5diff file1 file2
SEE ALSO h5dump(1), h5ls(1), h5repart(1), h5import(1), gif2h5(1), h52gif(1), h5perf(1)h5diff(1)
05-28-2016
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