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fix a typo of split
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sfchen committed Nov 26, 2017
1 parent e780193 commit 7ac1e68
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -7,7 +7,7 @@ This tool is designed to provide fast all-in-one preprocessing for FastQ files.
* correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality
* report JSON format result for further interpreting.
* visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative).
* split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total splitted file number, or limitting the lines of each splitted file.
* split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file.
* support long reads (data from PacBio / Nanopore devices).
* ...

Expand Down Expand Up @@ -97,7 +97,7 @@ options:
-w, --thread worker thread number, default is 3 (int [=3])

# output splitting options
-s, --split split output by limiting total splitted file number with this option (2~999), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (int [=0])
-s, --split split output by limiting total split file number with this option (2~999), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (int [=0])
-S, --split_by_lines split output by limiting lines of each file with this option(>=1000), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (long [=0])
-d, --split_prefix_digits the digits for the sequential number padding (1~10), default is 4, so the filename will be padded as 0001.xxx, 0 to disable padding (int [=4])

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2 changes: 1 addition & 1 deletion src/main.cpp
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Expand Up @@ -67,7 +67,7 @@ int main(int argc, char* argv[]){
cmd.add<int>("thread", 'w', "worker thread number, default is 3", false, 3);

// split the output
cmd.add<int>("split", 's', "split output by limiting total splitted file number with this option (2~999), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default", false, 0);
cmd.add<int>("split", 's', "split output by limiting total split file number with this option (2~999), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default", false, 0);
cmd.add<long>("split_by_lines", 'S', "split output by limiting lines of each file with this option(>=1000), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default", false, 0);
cmd.add<int>("split_prefix_digits", 'd', "the digits for the sequential number padding (1~10), default is 4, so the filename will be padded as 0001.xxx, 0 to disable padding", false, 4);

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