use heng li's fastx parser
remove multiline part 1
_int_quals_to_str_quals returns now str instead of iterator so that
get_str_quals always returns str data
some unnecesary join removed
get_len now uses strip instead of -1, in case there is no \n at the end
old functions eliminated
default parameters for pair_matcher changed
last_line[-1] changed for strip() in case there is no \n (in EOF)
get_len refactored to avoid duplicated code with get_str_seq
bug fix in a test and a runtimeerror added to avoid similar problems
groupby implementatio was slower so previous implementation remains
fastx itemizer switches to a faster implementation for single line fastq
Option to change buffer_size to check if pairs are ordered removed
KeyedSet class implemented
match_pairs uses KeyedSet instead of OrderedSet because set is faster
than bisect
unique_unordered implemented
filter_duplicates uses unique_unordered for high memory option (using
set is faster than sorting)
bug when getting paired_fpaths fixed and test added to detect it
map_process_to_bam split from map_with_bowtie2, so it now returns a
process that can be piped without writing a bam file
parallel_argparse changed to basic argparse
first version of filter_chimeras implemented
bwaws updated to new bwa mem algorithm
now mappping functions return mapping process and transformation to bam
file has been split to a new function for both bowtie2 and bwa.
readgroup option removed from map_with_bwamem
functions to sort sam/bam files implemented
new tests added
bwa updated to last version