now aligned_read_to_seqitem transforms into the complementary reverse
sequence if necessary
bugs fixed in aligned_read_to_seqitem
complementary now allows different letters to ATGC without changing them
(for N)
default tmpdir for sorting changed from None to /tmp
_get_possible_fragments corrected. It is even slower now
binary adapted to new algorithm
Changed chunk size when guessing format. It prevents failures in case
the description filed of a fasta file is too long
now aligned_read_to_seqitem does not require file format. It is assumed
to be fastq if there is quality information and fasta otherwise
add hability to add readgroup when writing the bam file of a map process
now sort_by_position_in_ref uses bowtie2 instead of bwa, because Bwa
returns a positioin for aligned_reads that are unmapped.
option for interleaved input seqs for map_with_bwa
Merge branch 'master' of ssh://gitolite@proxybioinf.comav.upv.es:2203/seq_crumbs
test modified to include option for low memory sorting
compile bwa with older libc version
Merge branch 'master' of ssh://gitolite@proxybioinf.comav.upv.es:2203/seq_crumbs
binary for chimeras trimming created
unnecessary imports removed
unpaired_fpaths and paired_fpaths interface restored back
Last version for filter_chimeras implemented
tests updated to new way of working
function to show distance between mate pairs distribution implemented
todo: add N binary
Merge branch 'master' of ssh://pb:2203/seq_crumbs
Option to select number of threads for mapping added to filter_chimeras
Merge branch 'master' of ssh://gitolite@proxybioinf.comav.upv.es:2203/seq_crumbs