BWA 0.5 and 0.5.5 are in-compatible

[Seq1234]

The alignments generated using 0.5.0 (.sai file)
gets corrupted when processed further using 0.5.5 version
for generating the .sam file.

for example for the sai file generated using the 0.5 version here is the output sam file

BTLM07P_FC42PBM_7_15_2_9 4 * 0 0 * * ...
BTLM07P_FC42PBM_7_15_2_A 16 Chr8 368744 0 100M ...

This is the correct result ...

where as when I used the 0.5.5 version to generate the sam file the output is as follows:

BTLM07P_FC42PBM_7_15_2_9 16 Chr8 368744 0 100M
BTLM07P_FC42PBM_7_15_2_A 4 * 0 0 * *

Notice the shifts in the alignments reported.

I expect all major users will re-use the .sai file for most of their analyses. Hence this can be big problem.

[lh3]

No, sai is a fast changing format and does not guarantee backward compatibility at all. One should not keep sai files. I always delete them when I get SAM output.

[maubp]

How about adding a version field to the SAI format to prevent this kind of mismatch (causing subtle corruption of data)? A clear error message would be much nicer.

[lh3]

Thanks. This is a good suggestion.