Add -v/--version option about fastp

[sfchen]

run fastp without any option, it will give you the version.

run fastp -? gives the same

[quantumdot]

I downloaded the pre-built binary located at http://opengene.org/fastp/fastp. Now that you mention it, running without any parameters, I see the version number output (0.12.2). Thanks for pointing this out. However, the -? or --help options do not generate the version message:

xxx@xxx[scripts] ./fastp --help                                                                                                                                                                                            
usage: ./fastp --in1=string [options] ...
options:
  -i, --in1                            read1 input file name (string)
  -o, --out1                           read1 output file name (string [=])
  -I, --in2                            read2 input file name (string [=])
  -O, --out2                           read2 output file name (string [=])
  -6, --phred64                        indicates the input is using phred64 scoring (it'll be converted to phred33, so the output will still be phred33)
  -z, --compression                    compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 2. (int [=2])
  -A, --disable_adapter_trimming       adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled
  -a, --adapter_sequence               the adapter for SE data, default is auto (automatic detection). For PE data adapters can be trimmed without knowing the sequences. (string [=auto])
  -f, --trim_front1                    trimming how many bases in front for read1, default is 0 (int [=0])
  -t, --trim_tail1                     trimming how many bases in tail for read1, default is 0 (int [=0])
  -F, --trim_front2                    trimming how many bases in front for read2. If it's not specified, it will follow read1's settings (int [=0])
  -T, --trim_tail2                     trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings (int [=0])
  -g, --trim_poly_g                    force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
  -G, --disable_trim_poly_g            disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
  -5, --cut_by_quality5                enable per read cutting by quality in front (5'), default is disabled (WARNING: this will interfere deduplication for both PE/SE data)
  -3, --cut_by_quality3                enable per read cutting by quality in tail (3'), default is disabled (WARNING: this will interfere deduplication for SE data)
  -W, --cut_window_size                the size of the sliding window for sliding window trimming, default is 4 (int [=4])
  -M, --cut_mean_quality               the bases in the sliding window with mean quality below cutting_quality will be cut, default is Q20 (int [=20])
  -Q, --disable_quality_filtering      quality filtering is enabled by default. If this option is specified, quality filtering is disabled
  -q, --qualified_quality_phred        the quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified. (int [=15])
  -u, --unqualified_percent_limit      how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40])
  -n, --n_base_limit                   if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5 (int [=5])
  -L, --disable_length_filtering       length filtering is enabled by default. If this option is specified, length filtering is disabled
  -l, --length_required                reads shorter than length_required will be discarded, default is 15. (int [=15])
  -c, --correction                     enable base correction in overlapped regions (only for PE data), default is disabled
  -U, --umi                            enable unique molecular identifer (UMI) preprocessing
      --umi_loc                        specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none (string [=])
      --umi_len                        if the UMI is in read1/read2, its length should be provided (int [=0])
      --umi_prefix                     if specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default (string [=])
  -p, --overrepresentation_analysis    enable overrepresented sequence analysis.
  -P, --overrepresentation_sampling    one in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20. (int [=20])
  -j, --json                           the json format report file name (string [=fastp.json])
  -h, --html                           the html format report file name (string [=fastp.html])
  -R, --report_title                   should be quoted with ' or ", default is "fastp report" (string [=fastp report])
  -w, --thread                         worker thread number, default is 3 (int [=3])
  -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])
  -?, --help                           print this message

xxx@xxx[scripts] ./fastp "-?"                                                                                                                                                                                              
usage: ./fastp --in1=string [options] ...
options:
  -i, --in1                            read1 input file name (string)
  -o, --out1                           read1 output file name (string [=])
  -I, --in2                            read2 input file name (string [=])
  -O, --out2                           read2 output file name (string [=])
  -6, --phred64                        indicates the input is using phred64 scoring (it'll be converted to phred33, so the output will still be phred33)
  -z, --compression                    compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 2. (int [=2])
  -A, --disable_adapter_trimming       adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled
  -a, --adapter_sequence               the adapter for SE data, default is auto (automatic detection). For PE data adapters can be trimmed without knowing the sequences. (string [=auto])
  -f, --trim_front1                    trimming how many bases in front for read1, default is 0 (int [=0])
  -t, --trim_tail1                     trimming how many bases in tail for read1, default is 0 (int [=0])
  -F, --trim_front2                    trimming how many bases in front for read2. If it's not specified, it will follow read1's settings (int [=0])
  -T, --trim_tail2                     trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings (int [=0])
  -g, --trim_poly_g                    force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
  -G, --disable_trim_poly_g            disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
  -5, --cut_by_quality5                enable per read cutting by quality in front (5'), default is disabled (WARNING: this will interfere deduplication for both PE/SE data)
  -3, --cut_by_quality3                enable per read cutting by quality in tail (3'), default is disabled (WARNING: this will interfere deduplication for SE data)
  -W, --cut_window_size                the size of the sliding window for sliding window trimming, default is 4 (int [=4])
  -M, --cut_mean_quality               the bases in the sliding window with mean quality below cutting_quality will be cut, default is Q20 (int [=20])
  -Q, --disable_quality_filtering      quality filtering is enabled by default. If this option is specified, quality filtering is disabled
  -q, --qualified_quality_phred        the quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified. (int [=15])
  -u, --unqualified_percent_limit      how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40])
  -n, --n_base_limit                   if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5 (int [=5])
  -L, --disable_length_filtering       length filtering is enabled by default. If this option is specified, length filtering is disabled
  -l, --length_required                reads shorter than length_required will be discarded, default is 15. (int [=15])
  -c, --correction                     enable base correction in overlapped regions (only for PE data), default is disabled
  -U, --umi                            enable unique molecular identifer (UMI) preprocessing
      --umi_loc                        specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none (string [=])
      --umi_len                        if the UMI is in read1/read2, its length should be provided (int [=0])
      --umi_prefix                     if specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default (string [=])
  -p, --overrepresentation_analysis    enable overrepresented sequence analysis.
  -P, --overrepresentation_sampling    one in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20. (int [=20])
  -j, --json                           the json format report file name (string [=fastp.json])
  -h, --html                           the html format report file name (string [=fastp.html])
  -R, --report_title                   should be quoted with ' or ", default is "fastp report" (string [=fastp report])
  -w, --thread                         worker thread number, default is 3 (int [=3])
  -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])
  -?, --help                           print this message

That being said, a dedicated --version flag would be greatly appreciated in that it simplifies machine parsing of the program version number for including this information in run logs. Thanks for your consideration of this enhancement.

[sfchen]

I see, I will make a update.

[sfchen]

Added -v/--version. Please try with the latest version.

[tseemann]

Ideally, the only output of fastp --version would be fastp 0.12.3 to stdout.

This is the de facto standard for most GNU tools and is easy for pipelines to parse.

[mblue9]

At the moment I'm extracting the version using fastp --version | tail -n 1 which is fine, but I agree with @tseemann that it would be good to just have the one line version output.
(hello @tseemann 👋)

[sfchen]

Implemented, now it's

fastp 0.19.0

[tseemann]

@sfchen unfortunately you did not follow the GNU standard.

It seems to print

fastp: an ultra-fast all-in-one FASTQ preprocessor
version 0.18.0

it should print

fastp 0.18.0

So it can be matched with the pattern /^NAME VERSION$/

[sfchen]

Are you trying the latest version?

Now it should be

fastp 0.19.0

[tseemann]

There is no 0.19.0 version yet. I can only package "Releases" and the latest is still 0.18.0.

[sfchen]

I will release v0.19.0 in this week.

[sfchen]

v0.19.3 released.