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Fix bug processing single-end bam files
The nbhd-snp parameter with single-end bam files (250) is read as string
which makes the round() function fail. Fixed by making the default
arguments as list so to have "auto" and 250 in the same object.
Add tests, bump version.
Fix bug in snp-pileup where arg 10000000 becomes 1e+07
snp-pileup was executed with argument `--max-depth 1e+07` which caused
wrong counts in the pileup table. The cause was R converting 10000000 to '1e+07'.
Fixed by making 10000000 part of the command string.
Add unit tests to catch the bug.
Bump version