inab/trimal

readAl/trimAl fails to output to nexus, mega and nbrf if sequences are classified 'Deg'

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Vicfero commented

If the input alignment (DNA/RNA) type is classified as DNADeg or RNADeg, both programs fail to output correctly:

NEXUS OUTPUT:

#NEXUS
BEGIN DATA;
DIMENSIONS NTAX=12 NCHAR=637;
;
...

NEXUS DESIRED OUTPUT

#NEXUS
BEGIN DATA;
DIMENSIONS NTAX=12 NCHAR=637;
FORMAT DATATYPE=DNA INTERLEAVE=yes GAP=-;

MEGA OUTPUT:

#MEGA
!Title dataset/huge/example4.sequential.phy.nexus;
NSeqs=12 Nsites=637 indel=- CodeTable=Standard;

MEGA DESIRED OUTPUT

#MEGA
!Title dataset/huge/example4.sequential.phy.nexus;
!Format DataType=DNA NSeqs=12 Nsites=637 indel=- CodeTable=Standard;

NBRF OUTPUT

>;VRA17
VRA17 637 bases

NBRF DESIRED OUTPUT

>DL;VRA17
VRA17 637 bases

The issue seems to be located on these lines:

  /* Compute output file datatype */
  getTypeAlignment();
  if (dataType == DNAType)
    alg_datatype = "DL";
  else if (dataType == RNAType)
    alg_datatype = "RL";
  else if (dataType == AAType)
    alg_datatype = "P1";

Degraded.zip