SWEMBL.3.5.delta
First attempt at SAM paired end import.
Read paired status of each read from SAM/BAM and use max of read length and fragment length.
Fixed fraglength bug and made BAM the default filetype.
Reading BAM paired-end and quality.
refsplit bugfix.
Before rewrite of count_sample_lines for BAM/SAM
After rewrite of count_sample_lines for BAM/SAM
Bug fix of switch breaks in BAM reading.
Streamline counting of BAM/SAM lines.
Can now overwrite individual -R parameters.
Fixed readline bug.
Fixed bug in number of SAM columns and unmapped reads flag.
Replace overall seq/fraglength with read's for paired-end.
Update reference_reads but NOT WORKING, ignoring ref reads.
Fixed reference read pairflag and seqlength bugs.
Fixed small bug in counting SAM/BAM reads with quality 0
Fixed bug in sorting reads for calculating reverse strand peaks
Fixed bugs in paired end read treatment. 1) Reads now sorted correctly. 2) Do not calculate read length for paired end BED files. 3) Altered treatment of BAM reads, so only counted if the difference in position of the next read is on same chromosome and greater than the position of the current read. 4) Reads mapping to the same start position, but different end positions now are treated as separately in the read counts. 5) When calling the peaks on the reverse strand, the threshold for read count at the same position is now applied correctly for the total reads mapping to either strand, not individually.
Added Apache software license.