[EMBOSS] diffseq -rformat seqtable dont report deletions correctly

[Tõnu]

Hi,

When to use the table output format (-rformat seqtable), diffseq
did not report deletions in one of a sequences correctly. It depend on
what order you give an input.

If deletion is in a second sequence (diffseq first.fa second.fa),
then table output is correct.
If deletion is in a first sequence (diffseq second.fa first.fa),
then deletion (marked with dot) is replaced with a letter and from
the tabel you can see nucleotide replacement.
I tried EMBOSS v. 2.6 (LINUX) and winemboss0.5 (v2.7)and both behave 
similarly.

Is it bug or is it feature?
If it is bug, how to fix it?



To illustrate situation look output.
Test sequences are listed too.

I  DELETION IN THE SECOND SEQ     CORRECT

diffseq  first.fa second.fa  -rformat seqtable -wordsize 3

#=======================================

   Start     End  start    end length name   sequence first_feature 
second_feature Sequence
      23      23     23     23      1 second a        .             
.              g
      71      71     70     69      . second .        .             
.              c
     470     470    469    469      1 second g        .             
.              a

#---------------------------------------


II DELETION IN THE FIRST  SEQ.   DEL IS NOT SEEN
first.fa pos 70C is replaced in this table wit second.fa 69T
Only thing that refers to deletion in the table is smaller end pos (69) 
than start pos (70).

diffseq  second.fa  first.fa  -rformat seqtable -wordsize 3

#=======================================

   Start     End  start    end length name   sequence first_feature 
second_feature Sequence
      23      23     23     23      1 first  g        .             
.              a
      70      69     71     71      1 first  c        .             
.              t
     469     469    470    470      1 first  a        .             
.              g

#---------------------------------------



test seqs are here

> first AY45
acaattgaatgtctgcacagccgctttccacacagacatcataacaaaaaatttccacca
aaccccccctccccccgcttctggccacagcacttaaacacatctctgccaaaccccaaa
aacaaagaaccctaacaccagcctaaccagatttcaaattttatcttttggcggtatgca
cttttaacagtcaccccccaactaacacattattttcccctcccactcccatactactaa
tctcatcaatacaacccccgcccatcctacccagcacacacacaccgctgctaaccccat
accccgaaccaaccaaaccccaaagacaccccccacagtttatgtagcttacctcctcaa
agcaatacactgaaaatgtttagacgggctcacatcaccccataaacaaataggtttggt
cctagcctttctattagctcttagtaagattacacatgcaagcatccccattccagtgag
ttcaccctctaaatcaccacgatcaaaagggacaagcatcaagcacgcagcaatgcagct
caaaacgcttagcctagccac

> second
acaattgaat
gtctgcacagccactttccacacagacatcataacaaaaaatttccacca
aaccccccctcccccgcttctggccacagcacttaaacacatctctgcca
aaccccaaaaacaaagaaccctaacaccagcctaaccagatttcaaattt
tatcttttggcggtatgcacttttaacagtcaccccccaactaacacatt
attttcccctcccactcccatactactaatctcatcaatacaacccccgc
ccatcctacccagcacacacacaccgctgctaaccccataccccgaacca
accaaaccccaaagacaccccccacagtttatgtagcttacctcctcaaa
gcaatacactgaaaatgtttagacgggctcacatcaccccataaacaaat
aggtttggtcctagcctttctattagctcttagtaagattacacatgcaa
gcatccccgttccagtgagttcaccctctaaatcaccacgatcaaaaggg
acaagcatcaagcacgcagcaatgcagctcaaaacgcttagcctagccac


Tõnu Margus
Estonian Biocentre
Riia 23
Tartu
Estonia
E-mail tmargus at ebc.ee