Initialise as a git repository.
Restarted git repository for this project to resolve conflict with git submodule in R/ folder.
Made SAM2MS.py output tab-separated. Started to implement other choices of CpG pairs for reads containing > 2 CpGs.
Added --ignore5 and --ignore3 options.
Added choice of algorithm (random, leftmost or outermost) for construction of CpG pairs.
Started a re-write of SAM2MS.py (SAM2MS_pysam.py) in order to utilise the pysam library.
SAM2MS.py is deprecated and renamed SAM2MS_deprecated.py
Development will continue on SAM2MS_pysam.py - the following comments refer to SAM2MS_pysam.py
SAM2MS_pysam.py is renamed BAM2MS.py to reflect the current features (and limitations) of the program
BAM2MS uses the pysam module which provides access to the SAMtools C-API
Fixed bug whereby reads mapped to the reverse strand would report the position of the guanine in the CpG rather than the cytosine. Now the co-ordinates of the CpG pair in the output file are the 1-based positions of the cytosines in each CpG in the pair.
Added documentation to BAM2MS.py on reads aligned to the reverse strand.
Clarification: "positions are 1-based positions of the cytosines on the forward strand in each CpG".
SAM files, as well as BAM files, can now be processed with the upgrade to pysam v0.6.
BAM2MS.py renamed to SAM2MS.py to reflect this.
Started to write paired-end version of SAM2MS.py in SAM2MS.py. Realised this is much more work than I thought so started it in it's own script PE_SAM2MS.py. These two scripts will be merged once both are stable.
Added strand information to output for SAM2MS.py.
Extensive update of PE_SAM2MS.py, however it still requires some notational tweaking and bug checks to ensure all possible read-pair MS combinations are correctly handled.
correct_Bismark_PE_SAM.py fixes the FLAG fields of a Bismark SAM/BAM file to ensure they compley with SAM spec v1.4.
SAM2MS.py has undergone minor changes.
summarise_MS.py collapses the output of SAM2MS.py or PE_SAM2MS.py on a CpG-pair basis.
lor_v3.R is the beginnings of a script to plot the output of summarise_MS.py
Simulation study to compare r^2, r and log-odds ratio as a measure of comethylation.
XM_tag.py is a python script to add the XM tag, which encodes the methylation state of bases along a read (see Bismark), to alignments generated by ANY bisulfite-sequencing aligner (e.g. BSMAP, NovoAlign). This tag has the same specification as implemented in Bismark.
Added argparse-r to corerct_Bismark_PE_SAM.py (untested).
Minor changes to the Python scripts. Added an R script to count the number of CpGs with x CpGs within a specified distance. This is useful for seeing getting an empirical view of CpG density in a genome.
Minor changes.
Added command line parsed to PE_SAM2MS.py
XM_parallel.sh is a simple shell script to process paired-end Bismark data with PE_SAM2MS.py on a chromosome-by-chromosome basis. This script probably won't work if there are read pairs aligned to different chromosomes.
Started writing QS_PE_SAM2MS.py, a script to extract the MS information from a query-name-sorted paired-end BAM file.
Working alpha version of QS_PE_SAM2MS.py. Assumes that the BAM contains ONLY properly paired-end reads and that the BAM is query-name-sorted.