first commit
uploading base files, runtophat.m not working yet
This version fixes a bug in the nested for loops in hash_sam_gene_align

The code is now working properly on basic examples. Tested functions are:
genecounts.m
runbowtie2.m
hash_sam_genealign.m
parse_gtf.m
set_pipeline_params.m
main_pipeline.m

To be tested:
runtophat.m
Began adding decsriptions to the functions within the README
Added description for convert_bam.m
Update
tested on:
aviv's single cell data
matt's cell types

changes made are so that pipeline works, no new functionality added
forgot to add sam_gene_align.m
forgot to add read_sam.cpp
Adding transcriptome index to repository
Added gene names (in the correct order) as a params field: params.gene_names_ordered
Added all_counts as a params field: params.allsamples
preparing pipeline for server useage

users now only must modify "set_user_params.m", they should no longer open "set_pipeline_params.m"
adding output filename as a param field
changes to run on server
changes to adapt to the server
adding the files from the server, this marks the begining of the repository