Spelling fix and version bump to 2.2.7

CRISPResso2/CRISPRessoPooledCORE.py

@@ -292,7 +292,7 @@ def main():
         parser.add_argument('--compile_postrun_reference_allele_cutoff', type=float, help='Only alleles with at least this percentage frequency in the population will be reported in the postrun analysis. This parameter is given as a percent, so 30 is 30%%.', default=30)
         parser.add_argument('--alternate_alleles', type=str, help='Path to tab-separated file with alternate allele sequences for pooled experiments. This file has the columns "region_name","reference_seqs", and "reference_names" and gives the reference sequences of alternate alleles that will be passed to CRISPResso for each individual region for allelic analysis. Multiple reference alleles and reference names for a given region name are separated by commas (no spaces).', default='')
         parser.add_argument('--limit_open_files_for_demux', help='If set, only one file will be opened during demultiplexing of read alignment locations. This will be slightly slower as the reads must be sorted, but may be necessary if the number of amplicons is greater than the number of files that can be opened due to OS constraints.', action='store_true')
-        parser.add_argument('--aligned_pooled_bam', type=str, help='Path to aligned input for CRISPRessoPooled processing. If this parameter is specified, the alignments in the given bam will be used to demultiplex reads. If this parameter is not set (default), input reads provided by --fastq_r1 (and optionally --fastq_r2) will be aligned to the reference genome using bowtie2. If the input bam is given, the corresponding reference fasta must also be given to extract reference genomic sequences via the parameter --bowtie2_index. Note that the aligned reads are paired-end seqenced, they should already be merged into 1 read (e.g. via Flash) before alignment.', default=None)
+        parser.add_argument('--aligned_pooled_bam', type=str, help='Path to aligned input for CRISPRessoPooled processing. If this parameter is specified, the alignments in the given bam will be used to demultiplex reads. If this parameter is not set (default), input reads provided by --fastq_r1 (and optionally --fastq_r2) will be aligned to the reference genome using bowtie2. If the input bam is given, the corresponding reference fasta must also be given to extract reference genomic sequences via the parameter --bowtie2_index. Note that the aligned reads are paired-end sequenced, they should already be merged into 1 read (e.g. via Flash) before alignment.', default=None)
         parser.add_argument('--demultiplex_only_at_amplicons', help='If set, and an amplicon file (--amplicons_file) and reference sequence (--bowtie2_index) are provided, reads overlapping alignment positions of amplicons will be demultiplexed and assigned to that amplicon. If this flag is not set, the entire genome will be demultiplexed and reads with the same start and stop coordinates as an amplicon will be assigned to that amplicon.', action='store_true')
 
         args = parser.parse_args()
@@ -1473,6 +1473,7 @@ def default_sigpipe():
 
         #cleaning up
         if not args.keep_intermediate:
+             info('Removing Intermediate files...')
 
              if args.fastq_r2!='':
                  files_to_remove+=[processed_output_filename, flash_hist_filename, flash_histogram_filename,\

CRISPResso2/CRISPRessoShared.py

@@ -25,7 +25,7 @@
 from CRISPResso2.CRISPRessoMultiProcessing import get_max_processes
 
 
-__version__ = "2.2.6"
+__version__ = "2.2.7"
 
 ###EXCEPTIONS############################
 class FlashException(Exception):