Update count_reads_aligned_to_de_novo_transcriptome.pl

# This script takes sam files (one per biological or technical replicate) and outputs tab separated list where the first column is the name of the contig and the values are the read counts per sample (in the same order as you listed your sam files)
# The script will print out sample ids. replace the example sample ids in line 17 with your own before running. This step is optional. Uncomment line 16 to 17 and lines 47 to 57 if you want these printed.