Fixing traceback of global alignments

[tbertelsen]

The traceback for global alignments is not created correctly.

Test case

(source):

>F12Fcsw_257171
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCT
CACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAATTCTTTTACCCCAGAACCATGTGATCCCGTGGTCTTA
TGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCTCGTCTGGGAAAGGGTTAGTCTCACGCGTTACTCCACCCGTCCCG
CCCGCCTAAAACAAAGCTCTAA
>M13Fcsw_294419
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCT
CACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCTCAGAACCATGTGATCCCGTGGTCTTA
TGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGGAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCT
AAAACAGCT

Alignment before change:

Alignment.getScore() = 175
Alignment.calculateScore() = 131

println(new String(alignment.getSequence1) + "\n" new String(alignment.getMarkupLine) + "\n" new String(alignment.getSequence2))

TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAATTCTTTTACCCCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCTCGTCTGGGAAAGGGTTAGTCTCACGCGTTACTCCACCCGTCCCGCCCGCCTAAAACAAAGCTCTAA
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.|||||||||.|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||..||||||||||||.|.............|...||..|||.|.|.....|....             
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCTCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGGAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAGCT-------------

Alignment after change:

Alignment.getScore() = 175
Alignment.calculateScore() = 175

println(new String(alignment.getSequence1) + "\n" new String(alignment.getMarkupLine) + "\n" new String(alignment.getSequence2))

TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAATTCTTTTACCCCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCTCGTCTGGGAAAGGGTTAGTCTCACGCGTTACTCCACCCGTCCCGCCCGCCTAAAACAAAGCTCTAA
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.|||||||||.|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||..||||||||||||.|   .||||||||||||||      .||||.|||||...||.|.||||    
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCTCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGGAAAGGTT---GCTCACGCGTTACTC------ACCCGTCCGCCGCTAAAACAGCT----