Remove unused scripts - Githubissues

Jylau14 / hyb2

A program for analyzing proximity ligation experiments from mapped files in the Fastq or SAM format to 1) generate a list of chimeric interactions with their coordinates, sequence, and folding energy, 2) plot contact density map of selected genes, 3) generate intra-/intermolecular RNA structure of any selected regions

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Remove unused scripts #10

Closed mwhamgenomics closed 1 year ago

mwhamgenomics commented 1 year ago

Several scripts in bin/ don't seem to be used anywhere. These should be removed, unless they are other entry points for the pipeline alongside bin/hyb2, in which case they should be documented:

chim_types
fasta2tab.sh
foldtest.sh
hybrid_stats_2 - see #8
inter_input.sh - all usages are commented out
lr_input.sh - all usages are commented out
make_bubble_array.sh
normalize_table_columns.awk
shuf
svg_mod_coord.sh
test_dcm

Jylau14 commented 1 year ago

Chim_types demonstrates the types of chimeras generated. Removed most unused scripts. Some will be used for future implementations.