Transit2

TRANSIT2:
- minor bug fix in 'cgi visualize'

Minor changes:

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Minor changes:
- updates to CGI functions (CRISPRi-DR) and documentation
- 'cgi extract_counts' can now process *.fastq.gz files (automatically unzips them)
- minor changes to how sgRNA ids are handled
- minor updates to format of input files like sgRNA_info.txt
- minor changes to command-line args and flags

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Minor changes:
- added empirical Bayes FDR analysis to filter significant interacting genes in CGI
- added '-no_uninduced' flag to CGI command (see documentation)

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Minor changes:
- fixed a bug that caused GUI to hang after popup windows were closed

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Minor changes:
- fixed a bug for making combined_wig files in GUI using gff files

TRANSIT2:

Minor changes:
- fix minor bug in CRISPRi-DR (cgi) output