Release 3.9.3

BugFix. Allow ARS values when w_reads is 0

BugFix. Unable to find ARS_table.txt after generating it

Bugfix. Problem with file names after trimming

This happened only after trimming single-end reads

BugFix. Problems with trim_galore file renaming

trim_galore names *_trimmed.fq.gz file names for single-end reads,
but it calls them *_val_1.fq.gz and *_val_2.fq.gz when presented
with parired-end reads
The MARIO program renames the val_1 and val_2 files to trimmed.fq.gz
The MARIO program was not saving the correctly renamed val_1 and val_2 files

BugFix. Problems with trim_galore file renaming

trim_galore names *_trimmed.fq.gz file names for single-end reads,
but it calls them *_val_1.fq.gz and *_val_2.fq.gz when presented
with parired-end reads
The MARIO program renames the val_1 and val_2 files to trimmed.fq.gz
The MARIO program was not saving the correctly renamed val_1 and val_2 files

BugFix. Failed producing multiple BED files

BED files compatible with IDR. Bugfixes

 Peak BED files now report entire MACS2 output (for compatibility with IDR
calculations) plus RPKMs and number of reads under peaks
 Expanded trimming capabilities: Trims adapter sequences if QC on reads fails
on "Per base sequence quality" and "Per sequence quality scores"
 Bugfix. Trimming failed when having paired-end reads due to file naming issues
 Bugfix. BAM sorting failed due changing option in samtools
(can only use samtools version 1.3 or higher now)
 Updated README.md
 Create CONFIG.txt instead of config_3.6.txt
 Better organization of the CONFIG.txt file

MD5 checksum check on downloaded SRA file

MD5 checksum check on downloaded SRA file