Fixed allele-assignment for certain SNPs in --bisulfite mode

v0.3.3

SNPsplit

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• Changed FindBin qw($Bin) to FindBin qw($RealBin) so that symlinks to tag2sort are resolved properly.

• In certain cases, specific SNPs were only used for the allele assignment if they were methylated. In more detail: In cases where the SNP was either C/G (REF/ALT) or G/C (REF/ALT), and the read was on the opposing strand, only the methylated form of the C on the reverse strand had previously been allowed as a valid expected base. This has now been changed so that both G and A are considered valid for the strain containing a G at the SNP position (see also this issue).

• Changed the way in which C>T SNPs are handled in the allele-tagging report (note that this was merely a report/interpretation thing and did not have any effect the on the actual results). Previously, reads without a call for genome 1 or genome 2 had been listed as:
  reads did not contain one of the expected bases at known SNP positions.
  In a bisulfite setting this also included C>T SNPs however, and hence the number could have been rather high (>10%). I have now changed this so that reads which had at least one C>T SNP and were unassignable at the same time are scored differently:
  reads that were unassignable contained C>T SNPs preventing the assignment

• Changed all instances of zcat to gunzip -c in SNPsplit and SNPsplit_genome_preparation to prevent errors on certain OSX platforms