INFO_FILENAME = 'info.txt'

# Default filenames

CDNA_FILENAME = 'cdna.fa'

INTRON_FILENAME = 'introns.fa'

SORTED_FASTA_FILENAME = 'sorted.fa'

SORTED_GTF_FILENAME = 'sorted.gtf'

COMBINED_FILENAME = 'combined.fa'

INDEX_FILENAME = 'transcriptome.idx'

WHITELIST_FILENAME = 'whitelist.txt'

FILTER_WHITELIST_FILENAME = 'filter_barcodes.txt'

INSPECT_FILENAME = 'inspect.json'

BUS_FILENAME = 'output.bus'

BUS_S_FILENAME = 'output.s.bus'

BUS_SC_FILENAME = 'output.s.c.bus'

BUS_UNFILTERED_FILENAME = 'output.unfiltered.bus'

BUS_FILTERED_FILENAME = 'output.filtered.bus'

BUS_CDNA_PREFIX = 'spliced'

BUS_INTRON_PREFIX = 'unspliced'

ECMAP_FILENAME = 'matrix.ec'

GENE_NAMES_FILENAME = 'genes.names.txt'

TXNAMES_FILENAME = 'transcripts.txt'

KB_INFO_FILENAME = 'kb_info.json'

KALLISTO_INFO_FILENAME = 'run_info.json'

REPORT_NOTEBOOK_FILENAME = 'report.ipynb'

REPORT_HTML_FILENAME = 'report.html'

COUNTS_PREFIX = 'cells_x_genes'

TCC_PREFIX = 'cells_x_tcc'

FEATURE_PREFIX = 'cells_x_features'

ADATA_PREFIX = 'adata'

GENE_NAME = 'gene'

FEATURE_NAME = 'feature'

TRANSCRIPT_NAME = 'transcript'

GENOMEBAM_FILENAME = 'pseudoalignments.bam'

GENOMEBAM_INDEX_FILENAME = 'pseudoalignments.bam.bai'

UNFILTERED_COUNTS_DIR = 'counts_unfiltered'

FILTERED_COUNTS_DIR = 'counts_filtered'

CELLRANGER_DIR = 'cellranger'

CELLRANGER_MATRIX = 'matrix.mtx'

CELLRANGER_BARCODES = 'barcodes.tsv'

CELLRANGER_GENES = 'genes.tsv'

BUS_UNFILTERED_SUFFIX = '.unfiltered.bus'

BUS_FILTERED_SUFFIX = '.filtered.bus'

# Bulk/Smartseq2 file names

FLENS_FILENAME = 'flens.txt'

BATCH_FILENAME = 'batch.txt'

ABUNDANCE_GENE_FILENAME = 'matrix.abundance.gene.mtx'

ABUNDANCE_GENE_NAMES_FILENAME = 'matrix.abundance.gene.names.mtx'

ABUNDANCE_GENE_TPM_FILENAME = 'matrix.abundance.gene.tpm.mtx'

ABUNDANCE_FILENAME = 'matrix.abundance.mtx'

ABUNDANCE_TPM_FILENAME = 'matrix.abundance.tpm.mtx'

FLD_FILENAME = 'matrix.fld.tsv'

CELLS_FILENAME = 'matrix.cells'

GENE_DIR = 'counts_gene'

GENES_FILENAME = 'genes.txt'

UNFILTERED_QUANT_DIR = 'quant_unfiltered'

SAVED_INDEX_FILENAME = 'index.saved'

# Smartseq3

INTERNAL_SUFFIX = '_internal'

UMI_SUFFIX = '_umi'

CAPTURE_FILENAME = 'capture_nonUMI.txt'

INSPECT_INTERNAL_FILENAME = 'inspect_internal.json'

INSPECT_UMI_FILENAME = 'inspect_umi.json'

# File codes.

# These are appended to the filename whenever it undergoes some kind of

# transformation.

SORT_CODE = 's'

CORRECT_CODE = 'c'

FILTERED_CODE = 'filtered'

UNFILTERED_CODE = 'unfiltered'

PROJECT_CODE = 'p'

# Loom

VELOCYTO_LOOM_NAMES = 'CellID,Gene'