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1 parent 2142b38 commit 7572821bcc65e74ceb1af1638bdf3b3e572c58cd @DrOppenheimer DrOppenheimer committed May 11, 2012
Showing with 4 additions and 8 deletions.
  1. +4 −8
@@ -75,7 +75,7 @@ Options:
Sequence type: fasta, fastq
Specify the type of sequence file; fasta and fastq are the only accepted options
- -f, --no_filter_seq [default True]
+ -f, --filter_seq [default True]
Run sequence filtering,
Sequence filtering performs two filtering processes before data are processed.
(1) An average and standard deviation is determined for the lengths of all reads.
@@ -86,9 +86,7 @@ Options:
the lower bound, are excluded from analysis. (2) Each remaining read is screened for
ambiguous bases ("N"). Reads with that possess a number of ambiguous bases that matches
or exceeds the specified limit (see -a AMBIG_MAX below)with -a AMBIG_MAX are excluded
- from further analysis. NOTE: that by default, no_filter is disabled. In this state,
- drisee __will__ perform filtering. Enabling this option will disable filtering
- (hence the long-option name, "no_filter").
+ from further analysis.
-r REP_FILE, --replicate_file=REP_FILE[default to calculate replicates]
List file with sorted indices for replicate bins. The file has one row for each read:
@@ -101,12 +99,10 @@ Options:
-l LOGFILE, --log_file=LOGFILE [default '/dev/null']
A detailed log of processing related statistics
- --no_percent [default True]
+ --percent [default True]
Produce second output profile with values presented
as percent per position. Additional output file is
- named "output_stat_file_pattern".per NOTE: that by default, no_percent is disabled. In this state,
- drisee __will__ produce a percent profile. Enabling this option will disable production of
- percent-based profiles (hence the long-option name, "no_pecent").
+ named "output_stat_file_pattern".per
--prefix_length=PREFIX [default 50]
Prefix length for the identification of bins of ADRs

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