MosaikAligner creates alignments that are incompatible with MosaikText

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What steps will reproduce the problem?
1. Run MosaikAligner
2. Run MosaikDupSnoop
3. Run MosaikSort

What is the expected output? What do you see instead?
I expect my alignment to be converted from .dat to .bam.  Instead, the program 
ends due to an error because the alignment contains an ambiguous nucleotide 
('S') that cannot be accepted in BAM format.  The ambiguous nucleotide is not 
found in my reference sequence, so it's something being created by 
MosaikAligner.

What version of the product are you using? On what operating system?
Mosaik 1.0.1388 on Red Hat Linux

Please provide any additional information below.
The commands I:m using are:
$ MosaikAligner -in mosaik_read_index -out bt_mosaiked.dat -ia 
~/data/refseq/mosaik_index/bos_taurus_cs.dat -ibs 
~/data/refseq/mosaik_index/bos_taurus_nt.dat -m unique -hs 11 -p 12 -act 15 -mm 
7 -mhp 500 -gep 6 
$ MosaikDupSnoop -in bt_mosaiked.dat -od dups
$ MosaikSort -consed -dup dups -in bt_mosaiked.dat -out bt_mosaiked_sorted.dat

Which gives the output:
------------------------------------------------------------------------------
MosaikText 1.0.1388                                                 2010-02-01
Michael Stromberg                 Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- converting the alignment archive to the following formats: BAM
Converting alignment archive:
19% [================>                                                          
                   ]  93,868.6 alignments/s       ETA 23 s \
ERROR: Only the following bases are supported in the BAM format: {=, A, C, G, 
T, N}. Found [S]

Original issue reported on code.google.com by rene.mal...@gmail.com on 12 Jul 2010 at 8:16