deprecated_scripts.md

#Scripts that have been deprecated: chain2psl bam2UniquePairs bam2libtype bam2peakshape bed2annotator bed2plot cat_tables cgat_fasta2cDNA combine_tables csv_interestion csv_rename csv_select csv_set medip_merge_intervals rndomize_lines transfac2transfac

Warnings for deprecation in the next release

AGP.py (its used once in gff2gff to parse agp files) Blat.py gff2psl