RELEASE NOTES FOR SHERMAN v0.1.7 (11 Aug 2014) ---------------------------------------------- Fixed a 1-off length issue for sequences with variable length adapter contamination. RELEASE NOTES FOR SHERMAN v0.1.6 (09 Sep 2013) ---------------------------------------------- Fixed some bugs with the length of the quality string that were inadvertently introduced in the pervious releases. This includes sequences with too short quality strings as well as the correct location of simulated single-end reads which were 1bp too long. RELEASE NOTES FOR SHERMAN v0.1.5 (24 Jul 2013) ---------------------------------------------- Fixed a bug which generated a too long sequence in --CR 0 mode. Also, the quality scores are now are now also truncated by 1bp again so that the sequence and the quality score strings have the same length. RELEASE NOTES FOR SHERMAN v0.1.4 (11 Jul 2013) ---------------------------------------------- For context specific cytosine conversion, Sherman assumed for simplicity that a C in the last position was in CH context. This did however cause a weird blip in the M-bias plots of simulated data at the end or read 1 and at the start of read 2. To account for this, Sherman does now internally generate a sequence that is 1bp longer than intended, and shortens it again after the bisulfite conversion step. Eventually, this change should only be noticable in an M-bias plot. RELEASE NOTES FOR SHERMAN v0.1.3 (18 Dec 2012) ---------------------------------------------- Changed the third line of basespace FastQ reads to be a "+" only, instead of printing the count (and read number) as this seems to crash other programs such as Cutadapt. RELEASE NOTES FOR SHERMAN v0.1.2 (05 Sep 2012) ---------------------------------------------- If reads are simulated from an existing genome, the genomic location of reads is printed into the read-ID line in addition to the read count number. This is to facilitate evaluations of different aligners. RELEASE NOTES FOR SHERMAN v0.1.1 (09 Jan 2012) ---------------------------------------------- The bisulfite conversion rate can now be any float number between 0 and 100% (instead of integers only). When reading in the reference genome, Sherman does now delete \r line endings in addition to \n which could occur when the reference was edited on a system such as Windows. Also, a "die" statement whenever a base other than A, C, T or G was encountered during the introduction of errors was changed into a warning instead (and an A will be introduced instead). Fixed a bug while generating non-directional paired-end libraries. This feature is now working as intended. RELEASE NOTES FOR SHERMAN v0.1.0 (15 Jul 2011) ---------------------------------------------- SHERMAN v0.1.0 is an initial beta release and as such is still a work in progress. We have successfully tested Sherman's output to produce accurate methylation data and contaminants with Bismark and FastQC, for the mouse and human genomes. We have initially designed Sherman to generate the kinds of library contaminations we were interested in, but if you have some ideas or suggestions which could be implemented we would love to hear from you. You can report feedback or bugs directly to: felix.krueger@babraham.ac.uk