Trying to understand perl error


 
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# 1  
Old 08-29-2016
Trying to understand perl error

I am trying to begin to troubleshoot this perl error that I keep getting, yet I get output is produced. The error is Use of uninitialized value in join or string line 175, <MANNO> line 7138 and below is line 175:

I am not too sure what the error is but since not every line has an error on it, I suspect maybe null values may be causing the issue. Thank you Smilie.

Code:
if (@prefield and join ("\t", @field[@name+3 .. $#field]) eq join ("\t", @prefield[@name+3 .. $#field])) { #same locus, multiple alternative allele

input
Code:
chr1    949608    .    G    A    3843.99    PASS    AF=1;AO=1297;DP=1303;FAO=399;FDP=399;FR=.;FRO=0;FSAF=204;FSAR=195;FSRF=0;FSRR=0;FWDB=0.0462861;FXX=0.00249994;HRUN=1;LEN=1;MLLD=151.783;OALT=A;OID=.;OMAPALT=A;OPOS=949608;OREF=G;PB=0.5;PBP=1;QD=38.5362;RBI=0.0475491;REFB=0;REVB=-0.0108863;RO=3;SAF=657;SAR=640;SRF=1;SRR=2;SSEN=0;SSEP=0;SSSB=0.000764295;STB=0.5;STBP=1;TYPE=snp;VARB=8.63542e-06;ANN=ISG15    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:181:1303:399:3:0:1297:399:1:640:657:1:2:195:204:0:0    GOOD    399    hom    116
chr1    949654    .    A    G    3787.59    PASS    AF=1;AO=1352;DP=1360;FAO=397;FDP=397;FR=.;FRO=0;FSAF=185;FSAR=212;FSRF=0;FSRR=0;FWDB=0.003541;FXX=0.00749981;HRUN=1;LEN=1;MLLD=133.768;OALT=G;OID=.;OMAPALT=G;OPOS=949654;OREF=A;PB=0.5;PBP=1;QD=38.1622;RBI=0.0270794;REFB=0.0316329;REVB=-0.0268469;RO=6;SAF=679;SAR=673;SRF=2;SRR=4;SSEN=0;SSEP=0;SSSB=0.00142636;STB=0.5;STBP=1;TYPE=snp;VARB=-0.000104249;ANN=ISG15    GT:GQ:DP:FDP:RO:FRO:AO:FAO:AF:SAR:SAF:SRF:SRR:FSAR:FSAF:FSRF:FSRR    1/1:161:1360:397:6:0:1352:397:1:673:679:2:4:212:185:0:0    GOOD    397    hom    115
chr1    955597    .    G    T    555.77    PASS

# 2  
Old 08-30-2016
Just a wild guess: (@name+3) means "length of array @name, plus 3". Could it be, that for some lines, this number is larger than $#field? Also, is it guaranteed that @prefield always has at least as many elements as @field? Maybe you could check these conditions before doing the join.
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