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HH= H¸@HѺHY̿P= 9u= HH= HHHH@Hw= HHǸ7XXHV= H¸@HѺHX蓫H> C> HHWH> > HHWH> > HHWH> d> HHeWHn> H> HHIWHZ> ,> HH-WHF> DžH> HcHHH= HcHHH= HcHHH= HcHHH= HcHHH= HcHHHK= 98H; H¸2@HѺHVE<#tHHH< H?HUHuøHؿHؿ@DžH< HcHHH< HcHHʋ H< HcHH4Hw< HcHHʋHd< HcHHʋH< HcHHHHؿHH螯; 91HؿHH; HH; H@HѺ&H[UDžwHؿHHcHHH@H; HcHHDHe; HcHHDHC; HcHHЋ8H"; HcHHDH; HcHHDH: HcHHHH: HcHHHo@H: DL$DD$<$EEHǸSH: HcHHHHt6H: HcHHH@H : HHǸ`SH : Hƿ R: 9w@YRDžVHؿHHcHHH@H9 HcHHDH9 HcHHЋ8H9 HcHHDH9 HcHHDH^9 HcHHЋH59 HcHHHH9 HcHHH0o@DD$<$EHǸQH9 HcHHHHt/H8 HcHHH@HHǸEQ P8 9HudH34%(tPÐHl$Ld$H-3 L%|3 Ll$Lt$L|$H\$H8L)AIHIPHt1@LLDAHH9uH\$Hl$Ld$Ll$ Lt$(L|$0H8ÐUHSHH2 Ht(`DHHHuH[]ÐHQH%s: [-g gap_score] [-a match_score] [-i mismatch_score] [-n] sequence_1 sequence2 -g, gap_score n aligns with a gap score of n (should be negative to act as a penalty) -a, match_score n aligns with a match score of n (should be positive to encourage matching) -i, mismatch_score n aligns with a mismatch score of n -n, no header does not print initial line with counts of mismatches, insertions, and deletes Default scores are gap: -1, match: 5, mismatch: -1 didn't find max: %d %d %d usage: %s [-s stats_file] [-a align_file] [-f] [-c cutoff] [-n k] [-m min] [-o output_file] [input_file] input_file gives a list of sequences with respective counts to be clustered; if no input_file specified, reads from stdin -s FILE calculates additional statistics and outputs them to FILE -a FILE stores alignment results in FILE -f forces entries to be clustered to, at most, one core -c N only performs alignments if align score is at least N -n N aligns the top N candidates during the aligning phase; defaults to 0 to skip aligning -m N a minimum of N counts will be required for a sequence to become a core -o FILE additionally outputs results to FILEWarning: an entry is not in expected format (sequence count) Warning: an entry has a non-positive count associated with it: %s %d ACGTNAligning remaining sequences... %d of %d entries [%d%%] #Alignment score cutoff: %d Aligned top %d candidates #Aligned sequences: %d Unaligned sequences: %d #Average best-alignment score: %d #Core sequence Core count Aligning sequence Align seq count Score %s %d %s %d %d help?w%s: Could not open statistics file %s for writing %s: Could not open align file %s for writing %s: Only positive align score cutoffs allowed %s: Only positive n allowed for aligning top n candidates %s: Only positive count mins allowed Could not open %s for writing %s: Unrecognized command line option (%c) s:fc:n:a:m:o:r%s: Could not access file %s Building data from file... Finding mismatch counts... Forming initial clusters... (forced single clustering) Forming secondary clusters... #core sequence score total count core count mm1 count mm2 count [sequence:count:mmcount]... %s %d:%d %d %d %d %d %s:%d:%d%s %d:%d %d %d %d %d #core sequence score total count core count mm1 count mm2 count [sequence:count:mmcount]...Generating cluster statistics... %d of %d performed [%d%%] #Degeneracy Sequence Count Sequence Proximal Clusters Largest Proximal Cluster Smallest Proximal Cluster All proximal cluster sizes %d %d %s %d %d %d %d&@(@e'@(@(@V'@(@(@(@(@(@(@ (@'@^(@(@(@(@&@usage: %s [-i 5':3'] [-u n] [-f|q] [-o output_file] [-m S|X|I|J|L] [-c] [input_file] usage: %s [-i 5':3'] [-u n] [-f|q] [-o output_file] [-m S|X|I|J] [-c] [input_file] input_file specifies the file with entries either in qseq or fastq format; if none provided, reads stdin -i X:Y trim X bases on 5' end and Y bases on 3' end -u N truncate sequence to N bases -f force input file to be parsed as a fastq file -q force input file to be parsed as a qsec file -o FILE additionally prints results to FILE -m S|X|I|J filters by Sanger, Solexa, Illumina 1.3+, Illumina 1.5+ (respectively) -c only unfiltered results will be reported in output#trim: %d:%d #truncate: %d #quality lo: %d hi: %d adj: %d cutoff: %d #total reads: %d #unique reads: %d #filtered bases: %d #read count %s %d Sequence length and quality length mismatch ?helpwCould not access %s for writing Unrecognized quality filter method (%c) Invalid quality cutoff: %d i:u:fqo:m:crCould not read from file %s %s: Both fastq and qsec flags indicated Reading from stdin requires -f or -q Cannot determine file format of %s .fastq.fq.txtExpected .fastq/.fq or .txt file (%s) Could not determine input type (fastq or qseq) Y@Y@Y@W@Y@Y@*W@Y@Y@Y@,X@Y@W@Y@W@Y@Y@Y@W@X@X@X@X@X@X@X@X@X@X@QX@X@X@X@X@tX@usage: %s count|cluster|map|tabulate [OPTIONS]... countclustermaptabulateACGTNCould not allocate enough space Ran out of memory Usage: %s [-c min_count_cutoff] [-n align_top_n] [-o output_file] [-s] [cluster_file] barcode_file Generates a list of best-matching barcodes for each cluster sequencecluster_file specifies clusters to match to barcodes, if unspecified, will read stdinbarcode_file specifies barcodes available for matching -c CUTOFF clusters require a count of CUTOFF or more to be aligned -n N clusters try only to align to the top N candidate barcodes -o FILE additionally outputs results to FILE -s skips aligning clustersWarning: an entry is not in expected format (details sequence) %s Warning: there are non-unique barcode_sequences in the barcode file Warning: barcode sequence file has %dmer word overlaps Error: a cluster entry is not in the valid format: seq mm1n:mm2n mm0 mm1 mm2 Warning: an entry is not in expected format (sequence (cluster details)...) Warning: there are non-unique cluster cores in the cluster file Aligning remaining sequences (top %d candidates only)... %d of %d entries [%d%%] ;%d:%s:%d:%d:%d%s%d:%s:%d:%d:%dhelp?wCould not open %s for writing%s: Unknown parameter (%s) c:n:o:srNo cluster input file Could not open barcode file Building data from files... Performing mismatch matches... Skipping (clusters longer than barcodes) Skipping alignments #contains: %d # mm0s: %d # mm1s: %d # mm2s: %d #aligns: %d #misses: %d #core seq count score mm0 mm1n mm1 mm2n mm2 match id seq [score:alignment:mis:ins:del]... %s %d %d:%d %d %d %d %d %d nonemm0 mm1 mm2 align N/A %s %sMULTIPLE: %s#core seq count score mm0 mm1n mm1 mm2n mm2 match id seq [score:alignment:mis:ins:del]...%sACGTNUsage: %s [-c align_cutoff] [-o output_file] [map_file] barcode_file Usage: %s [map_file] barcode_file Matches the mapped clusters to the barcodes of interestmap_file specifies the mapped clusters; if unspecified, will read from stdinbarcode_file specifies the barcodes of interest -c N Align score needs to be at least N to match a barcode, default is %d Warning: an entry is not in expected format (sequence details) Warning: there are non-unique barcode_sequences in the barcode file Error: a map entry is not in the valid format: seq total score mm0 mm1n mm1 mm2n mm2 match type barcode id barcode seq aligns nonealignmm0mm1mm2;help?wCould not open %s for writing%s: Unknown parameter (%s) c:n:o:rNo map file supplied Could not open barcode file %s Building barcodes... 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