added	.gitignore
added	README.md
added	annotate_mouse_transcriptome.py
added	annotate_transcriptome.py
added	bins/trimmomatic-0.33.jar
added	count_barcode_distribution.py
added	default_parameters.yaml
added	indrops.py
added	quantify_umifm_from_alignments.py
added	ref/barcode_lists/gel_barcode1_list.txt
added	ref/barcode_lists/gel_barcode2_list.txt
added	test/seq_runs/run_v1_single_file/R1.fastq.gz
added	test/seq_runs/run_v1_single_file/R2.fastq.gz
added	test/seq_runs/run_v2_single_file/R1.fastq.gz
added	test/seq_runs/run_v2_single_file/R2.fastq.gz
added	test/seq_runs/run_v2_split/lib1_L001_R1_001.fastq copy
added	test/seq_runs/run_v2_split/lib1_L001_R1_001.fastq copy.gz
added	test/seq_runs/run_v2_split/lib1_L001_R1_001.fastq.gz
added	test/seq_runs/run_v2_split/lib1_L001_R2_001.fastq.gz
added	test/seq_runs/run_v2_split/lib1_L002_R1_001.fastq.gz
added	test/seq_runs/run_v2_split/lib1_L002_R2_001.fastq.gz
added	test/seq_runs/run_v2_split/lib1_L003_R1_001.fastq.gz
added	test/seq_runs/run_v2_split/lib1_L003_R2_001.fastq.gz
added	test/seq_runs/run_v2_split/lib1_L004_R1_001.fastq.gz
added	test/seq_runs/run_v2_split/lib1_L004_R2_001.fastq.gz