[med-svn] [Git][med-team/seqkit][upstream] New upstream version 0.15.0+ds

Nilesh Patra gitlab at salsa.debian.org
Thu Jan 14 11:25:04 GMT 2021



Nilesh Patra pushed to branch upstream at Debian Med / seqkit


Commits:
8fdd687f by Nilesh Patra at 2021-01-14T16:34:12+05:30
New upstream version 0.15.0+ds
- - - - -


15 changed files:

- CHANGES.md
- doc/docs/download.md
- doc/docs/usage.md
- + go.mod
- + go.sum
- seqkit/cmd/amplicon.go
- seqkit/cmd/bam_toolbox.go
- seqkit/cmd/grep.go
- seqkit/cmd/locate.go
- seqkit/cmd/seq.go
- seqkit/cmd/shuffle.go
- seqkit/cmd/split2.go
- seqkit/cmd/version.go
- seqkit/packaging.sh
- tests/test.sh


Changes:

=====================================
CHANGES.md
=====================================
@@ -1,3 +1,11 @@
+- [SeqKit v0.15.0](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.15.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)
+    - `seqkit grep/locate`: update help message.
+    - `seqkit grep`: **search on both strand when searching by sequence**.
+    - `seqkit split2`: fix redundant log when using `-s`.
+    - `seqkit bam`: new field `RightSoftClipSeq`. [#172](https://github.com/shenwei356/seqkit/pull/172)
+    - `seqkit sample -2`: remove extra `\n`. [#173](https://github.com/shenwei356/seqkit/issues/173)
+    - `seqkit split2 -l`: fix bug for splitting by accumulative length, this bug occurs when the first record is longer than `-l`, no sequences are lost.
 - [SeqKit v0.14.0](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.14.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
     - new command `seqkit pair`: match up paired-end reads from two fastq files, faster than fastq-pair.


=====================================
doc/docs/download.md
=====================================
@@ -6,17 +6,14 @@ SeqKit is implemented in [Go](https://golang.org/) programming language,
 
 ## Latest Version
 
-- [SeqKit v0.14.0](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.14.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
-    - new command `seqkit pair`: match up paired-end reads from two fastq files, faster than fastq-pair.
-    - `seqkit translate`: new flag `-F/--append-fram` for optional adding frame info to ID. [#159](https://github.com/shenwei356/seqkit/issues/159)
-    - `seqkit stats`: reduce memory usage when using `-a` for calculating N50. [#153](https://github.com/shenwei356/seqkit/issues/153)
-    - `seqkit mutate`: fix inserting sequence `-i/--insertion`, 
-       this bug occurs when `insert site` is big in some cases, don't worry if no error reported.
-    - `seqkit replace`:
-        - new flag `-U/--keep-untouched`: do not change anything when no value found for the key (only for sequence name).
-        - do no support editing FASTQ sequence.
-    - `seqkit grep/locate`: new flag `--circular` for supporting circular genome. [#158](https://github.com/shenwei356/seqkit/issues/158)
+- [SeqKit v0.15.0](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.15.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)
+    - `seqkit grep/locate`: update help message.
+    - `seqkit grep`: **search on both strand when searching by sequence**.
+    - `seqkit split2`: fix redundant log when using `-s`.
+    - `seqkit bam`: new field `RightSoftClipSeq`. [#172](https://github.com/shenwei356/seqkit/pull/172)
+    - `seqkit sample -2`: remove extra `\n`. [#173](https://github.com/shenwei356/seqkit/issues/173)
+    - `seqkit split2 -l`: fix bug for splitting by accumulative length, this bug occurs when the first record is longer than `-l`, no sequences are lost.
 
 ### Please cite
 
@@ -33,12 +30,13 @@ SeqKit is implemented in [Go](https://golang.org/) programming language,
 
 OS     |Arch      |File, 中国镜像                                                                                                                                                                                  |Download Count
 :------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |32-bit    |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_linux_386.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz)                            |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_linux_386.tar.gz)
-Linux  |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_linux_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz)                  |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_linux_amd64.tar.gz)
-OS X   |32-bit    |[seqkit_darwin_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_darwin_386.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_386.tar.gz)                         |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_386.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_darwin_386.tar.gz)
-OS X   |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_darwin_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz)               |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_darwin_amd64.tar.gz)
-Windows|32-bit    |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_windows_386.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz)          |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_windows_amd64.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.14.0/seqkit_windows_amd64.exe.tar.gz)
+Linux  |32-bit    |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_linux_386.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz)                            |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_linux_386.tar.gz)
+Linux  |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_linux_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz)                  |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_linux_amd64.tar.gz)
+Linux  |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_linux_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz)                  |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_linux_arm64.tar.gz)
+macOS  |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_darwin_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz)               |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_darwin_amd64.tar.gz)
+macOS  |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_darwin_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz)               |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_darwin_arm64.tar.gz)
+Windows|32-bit    |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_windows_386.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz)          |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_windows_amd64.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/seqkit/releases/download/v0.15.0/seqkit_windows_amd64.exe.tar.gz)
 
 
 ## Installation
@@ -108,6 +106,17 @@ Howto:
 
 ## Release History
 
+- [SeqKit v0.14.0](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.14.0/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
+    - new command `seqkit pair`: match up paired-end reads from two fastq files, faster than fastq-pair.
+    - `seqkit translate`: new flag `-F/--append-fram` for optional adding frame info to ID. [#159](https://github.com/shenwei356/seqkit/issues/159)
+    - `seqkit stats`: reduce memory usage when using `-a` for calculating N50. [#153](https://github.com/shenwei356/seqkit/issues/153)
+    - `seqkit mutate`: fix inserting sequence `-i/--insertion`, 
+       this bug occurs when `insert site` is big in some cases, don't worry if no error reported.
+    - `seqkit replace`:
+        - new flag `-U/--keep-untouched`: do not change anything when no value found for the key (only for sequence name).
+        - do no support editing FASTQ sequence.
+    - `seqkit grep/locate`: new flag `--circular` for supporting circular genome. [#158](https://github.com/shenwei356/seqkit/issues/158)
 - [SeqKit v0.13.2](https://github.com/shenwei356/seqkit/releases/tag/v0.13.2)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v0.13.2/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v0.13.2)
     - `seqkit sana`: fix bug causing hanging on empty files. [#149](https://github.com/shenwei356/seqkit/pull/149)


=====================================
doc/docs/usage.md
=====================================
@@ -174,7 +174,7 @@ reproduced in different environments with same random seed.
 ``` text
 SeqKit -- a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
 
-Version: 0.14.0
+Version: 0.15.0
 
 Author: Wei Shen <shenwei356 at gmail.com>
 
@@ -283,6 +283,11 @@ Usage
 ``` text
 transform sequences (revserse, complement, extract ID...)
 
+Attentions:
+
+  1. This command outputs plain text even when out file ends with ".gz".
+
+
 Usage:
   seqkit seq [flags]
 
@@ -1372,12 +1377,20 @@ Attentions:
   1. Unlike POSIX/GNU grep, we compare the pattern to the whole target
      (ID/full header) by default. Please switch "-r/--use-regexp" on
      for partly matching.
-  2. While when searching by sequences, only positive strand is searched,
-     and it's partly matching. 
+  2. When searching by sequences, it's partly matching, and both positive
+     and negative strands are searched.
      Mismatch is allowed using flag "-m/--max-mismatch",
      but it's not fast enough for large genome like human genome.
      Though, it's fast enough for microbial genomes.
-  3. The order of sequences in result is consistent with that in original
+  3. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
+     But do not use degenerate bases/residues in regular expression, you need
+     convert them to regular expression, e.g., change "N" or "X"  to "."..
+  4. When providing search patterns (motifs) via flag '-p',
+     please use double quotation marks for patterns containing comma, 
+     e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
+     parser accepts comma-separated-values (CSV) for multiple values (motifs).
+     Patterns in file do not follow this rule.
+  5. The order of sequences in result is consistent with that in original
      file, not the order of the query patterns. 
      But for FASTA file, you can use:
         seqkit faidx seqs.fasta --infile-list IDs.txt
@@ -1404,26 +1417,27 @@ Usage:
   seqkit grep [flags]
 
 Flags:
-  -n, --by-name               match by full name instead of just ID
-  -s, --by-seq                search subseq on seq, only positive strand is searched, and mismatch allowed using flag -m/--max-mismatch
-  -c  --circular              circular genome
-  -d, --degenerate            pattern/motif contains degenerate base
-      --delete-matched        delete a pattern right after being matched, this keeps the firstly matched data and speedups when using regular expressions
-  -h, --help                  help for grep
-  -i, --ignore-case           ignore case
-  -v, --invert-match          invert the sense of matching, to select non-matching records
-  -m, --max-mismatch int      max mismatch when matching by seq. For large genomes like human genome, using mapping/alignment tools would be faster
-  -p, --pattern strings       search pattern (multiple values supported. Attention: use double quotation marks for patterns containing comma, e.g., -p '"A{2,}"'))
-  -f, --pattern-file string   pattern file (one record per line)
-  -R, --region string         specify sequence region for searching. e.g 1:12 for first 12 bases, -12:-1 for last 12 bases
-  -r, --use-regexp            patterns are regular expressio
+  -n, --by-name                match by full name instead of just ID
+  -s, --by-seq                 search subseq on seq, both positive and negative strand are searched, and mismatch allowed using flag -m/--max-mismatch
+  -c, --circular               circular genome
+  -d, --degenerate             pattern/motif contains degenerate base
+      --delete-matched         delete a pattern right after being matched, this keeps the firstly matched data and speedups when using regular expressions
+  -h, --help                   help for grep
+  -i, --ignore-case            ignore case
+  -v, --invert-match           invert the sense of matching, to select non-matching records
+  -m, --max-mismatch int       max mismatch when matching by seq. For large genomes like human genome, using mapping/alignment tools would be faster
+  -P, --only-positive-strand   only search on positive strand
+  -p, --pattern strings        search pattern (multiple values supported. Attention: use double quotation marks for patterns containing comma, e.g., -p '"A{2,}"'))
+  -f, --pattern-file string    pattern file (one record per line)
+  -R, --region string          specify sequence region for searching. e.g 1:12 for first 12 bases, -12:-1 for last 12 bases
+  -r, --use-regexp             patterns are regular expression
 
 ```
 
 Examples
 
 
-1. Searching with list of sequence IDs (do not containing whitespace)
+1. Searching with list of sequence IDs (do not contain whitespace)
 
         $ seqkit grep -f id.txt seqs.fq.gz -o result.fq.gz
         
@@ -1526,20 +1540,23 @@ Usage
 ``` text
 locate subsequences/motifs, mismatch allowed
 
-Motifs could be EITHER plain sequence containing "ACTGN" OR regular
-expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.
-Degenerate bases like "RYMM.." are also supported by flag -d.
-
-By default, motifs are treated as regular expression.
-When flag -d given, regular expression may be wrong.
-For example: "\w" will be wrongly converted to "\[AT]".
-
-Mismatch is allowed using flag "-m/--max-mismatch",
-but it's not fast enough for large genome like human genome.
-Though, it's fast enough for microbial genomes.
+Attentions:
 
-When using flag --circular, end position of matched subsequence that 
-crossing genome sequence end would be greater than sequence length.
+  1. Motifs could be EITHER plain sequence containing "ACTGN" OR regular
+     expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.     
+  2. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
+     But do not use degenerate bases/residues in regular expression, you need
+     convert them to regular expression, e.g., change "N" or "X"  to "."..
+  3. When providing search patterns (motifs) via flag '-p',
+     please use double quotation marks for patterns containing comma, 
+     e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
+     parser accepts comma-separated-values (CSV) for multiple values (motifs).
+     Patterns in file do not follow this rule.     
+  4. Mismatch is allowed using flag "-m/--max-mismatch",
+     but it's not fast enough for large genome like human genome.
+     Though, it's fast enough for microbial genomes.
+  5. When using flag --circular, end position of matched subsequence that 
+     crossing genome sequence end would be greater than sequence length.
 
 Usage:
   seqkit locate [flags]
@@ -1760,6 +1777,9 @@ retrieve amplicon (or specific region around it) via primer(s).
 Attentions:
   1. Only one (the longest) matching location is returned for every primer pair.
   2. Mismatch is allowed, but the mismatch location (5' or 3') is not controled. 
+  3. Degenerate bases/residues like "RYMM.." are also supported.
+     But do not use degenerate bases/residues in regular expression, you need
+     convert them to regular expression, e.g., change "N" or "X"  to "."..
 
 Examples:
   0. no region given.
@@ -1809,16 +1829,17 @@ Usage:
   seqkit amplicon [flags]
 
 Flags:
-      --bed                    output in BED6+1 format with amplicon as 7th column
+      --bed                    output in BED6+1 format with amplicon as 7th columns
   -f, --flanking-region        region is flanking region
-  -F, --forward string         forward primer (5'-primer-3')
+  -F, --forward string         forward primer (5'-primer-3'), degenerate bases allowed
   -h, --help                   help for amplicon
-  -m, --max-mismatch int       max mismatch when matching primers
+  -m, --max-mismatch int       max mismatch when matching primers, no degenerate bases allowed
   -P, --only-positive-strand   only search on positive strand
   -p, --primer-file string     3- or 2-column tabular primer file, with first column as primer name
   -r, --region string          specify region to return. type "seqkit amplicon -h" for detail
-  -R, --reverse string         reverse primer (5'-primer-3')
+  -R, --reverse string         reverse primer (5'-primer-3'), degenerate bases allowed
   -s, --strict-mode            strict mode, i.e., discarding seqs not fully matching (shorter) given region range
+
 ```
 
 Examples
@@ -2181,7 +2202,7 @@ Usage:
   seqkit split2 [flags]
 
 Flags:
-  -l, --by-length string   split sequences into chunks of N bases, supports K/M/G suffix
+  -l, --by-length string   split sequences into chunks of >=N bases, supports K/M/G suffix
   -p, --by-part int        split sequences into N parts
   -s, --by-size int        split sequences into multi parts with N sequences
   -f, --force              overwrite output directory


=====================================
go.mod
=====================================
@@ -0,0 +1,36 @@
+module github.com/shenwei356/seqkit
+
+go 1.16
+
+require (
+	github.com/biogo/biogo v1.0.3
+	github.com/biogo/hts v1.2.2
+	github.com/bsipos/thist v1.0.0
+	github.com/cespare/xxhash v1.1.0
+	github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548 // indirect
+	github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8
+	github.com/dustin/go-humanize v1.0.0
+	github.com/edsrzf/mmap-go v1.0.0 // indirect
+	github.com/fsnotify/fsnotify v1.4.9
+	github.com/iafan/cwalk v0.0.0-20191125092548-dd7f505d2f66
+	github.com/klauspost/compress v1.11.4 // indirect
+	github.com/klauspost/pgzip v1.2.5 // indirect
+	github.com/logrusorgru/aurora v2.0.3+incompatible
+	github.com/mattn/go-colorable v0.1.8
+	github.com/mattn/go-isatty v0.0.12
+	github.com/mattn/go-runewidth v0.0.9 // indirect
+	github.com/mitchellh/go-homedir v1.1.0
+	github.com/pkg/errors v0.9.1
+	github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect
+	github.com/shenwei356/bio v0.0.0-20201213090627-18e3e643a476
+	github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403 // indirect
+	github.com/shenwei356/breader v0.0.0-20170924140440-21f0a70fe179
+	github.com/shenwei356/bwt v0.0.0-20200418151221-ae79c9858c90
+	github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba
+	github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d // indirect
+	github.com/shenwei356/util v0.0.0-20201214054755-2942125340cd
+	github.com/shenwei356/xopen v0.0.0-20181203091311-f4f16ddd3992
+	github.com/smallfish/simpleyaml v0.0.0-20170911015856-a32031077861
+	github.com/spf13/cobra v1.1.1
+	github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939
+)


=====================================
go.sum
=====================================
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+gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 h1:YR8cESwS4TdDjEe65xsg0ogRM/Nc3DYOhEAlW+xobZo=
+gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+gopkg.in/errgo.v2 v2.1.0/go.mod h1:hNsd1EY+bozCKY1Ytp96fpM3vjJbqLJn88ws8XvfDNI=
+gopkg.in/ini.v1 v1.51.0/go.mod h1:pNLf8WUiyNEtQjuu5G5vTm06TEv9tsIgeAvK8hOrP4k=
+gopkg.in/resty.v1 v1.12.0/go.mod h1:mDo4pnntr5jdWRML875a/NmxYqAlA73dVijT2AXvQQo=
+gopkg.in/yaml.v2 v2.0.0-20170812160011-eb3733d160e7/go.mod h1:JAlM8MvJe8wmxCU4Bli9HhUf9+ttbYbLASfIpnQbh74=
+gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
+gopkg.in/yaml.v2 v2.2.4/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
+gopkg.in/yaml.v2 v2.2.8 h1:obN1ZagJSUGI0Ek/LBmuj4SNLPfIny3KsKFopxRdj10=
+gopkg.in/yaml.v2 v2.2.8/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
+honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
+honnef.co/go/tools v0.0.0-20190106161140-3f1c8253044a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
+honnef.co/go/tools v0.0.0-20190418001031-e561f6794a2a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
+honnef.co/go/tools v0.0.1-2019.2.3/go.mod h1:a3bituU0lyd329TUQxRnasdCoJDkEUEAqEt0JzvZhAg=
+rsc.io/binaryregexp v0.2.0/go.mod h1:qTv7/COck+e2FymRvadv62gMdZztPaShugOCi3I+8D8=
+rsc.io/pdf v0.1.1 h1:k1MczvYDUvJBe93bYd7wrZLLUEcLZAuF824/I4e5Xr4=
+rsc.io/pdf v0.1.1/go.mod h1:n8OzWcQ6Sp37PL01nO98y4iUCRdTGarVfzxY20ICaU4=


=====================================
seqkit/cmd/amplicon.go
=====================================
@@ -51,6 +51,9 @@ var ampliconCmd = &cobra.Command{
 Attentions:
   1. Only one (the longest) matching location is returned for every primer pair.
   2. Mismatch is allowed, but the mismatch location (5' or 3') is not controled. 
+  3. Degenerate bases/residues like "RYMM.." are also supported.
+     But do not use degenerate bases/residues in regular expression, you need
+     convert them to regular expression, e.g., change "N" or "X"  to "."..
 
 Examples:
   0. no region given.
@@ -135,7 +138,7 @@ Examples:
 			list, err = loadPrimers(primerFile)
 			checkError(err)
 		} else {
-			list = [][3]string{[3]string{".", forward0, reverse0}}
+			list = [][3]string{{".", forward0, reverse0}}
 		}
 
 		primers, err = parsePrimers(list)
@@ -261,7 +264,7 @@ func init() {
 
 	ampliconCmd.Flags().StringP("forward", "F", "", "forward primer (5'-primer-3'), degenerate bases allowed")
 	ampliconCmd.Flags().StringP("reverse", "R", "", "reverse primer (5'-primer-3'), degenerate bases allowed")
-	ampliconCmd.Flags().IntP("max-mismatch", "m", 0, "max mismatch when matching primers")
+	ampliconCmd.Flags().IntP("max-mismatch", "m", 0, "max mismatch when matching primers, no degenerate bases allowed")
 	ampliconCmd.Flags().StringP("primer-file", "p", "", "3- or 2-column tabular primer file, with first column as primer name")
 
 	ampliconCmd.Flags().StringP("region", "r", "", `specify region to return. type "seqkit amplicon -h" for detail`)
@@ -374,6 +377,9 @@ func NewAmpliconFinder(sequence, forwardPrimer, reversePrimerRC []byte, maxMisma
 		finder.FMindex = index
 	} else {
 		if seq.DNA.IsValid(finder.F) != nil { // containing degenerate base
+			if maxMismatch > 0 {
+				checkError(fmt.Errorf("it does not support both degenerate base and mismatch"))
+			}
 			s, _ := seq.NewSeq(seq.DNA, finder.F)
 			rF, err := regexp.Compile(s.Degenerate2Regexp())
 			if err != nil {
@@ -383,6 +389,9 @@ func NewAmpliconFinder(sequence, forwardPrimer, reversePrimerRC []byte, maxMisma
 		}
 
 		if seq.DNA.IsValid(finder.R) != nil { // containing degenerate base
+			if maxMismatch > 0 {
+				checkError(fmt.Errorf("it does not support both degenerate base and mismatch"))
+			}
 			s, _ := seq.NewSeq(seq.DNA, finder.R)
 			rR, err := regexp.Compile(s.Degenerate2Regexp())
 			if err != nil {


=====================================
seqkit/cmd/bam_toolbox.go
=====================================
@@ -457,7 +457,7 @@ func GetSamAlnDetails(r *sam.Record) *AlnDetails {
 }
 
 func BamToolDump(p *BamToolParams) {
-	validFields := []string{"Read", "Ref", "Pos", "EndPos", "MapQual", "Acc", "Match", "Mismatch", "Ins", "Del", "AlnLen", "ReadLen", "RefLen", "RefAln", "RefCov", "ReadAln", "ReadCov", "Strand", "MeanQual", "LeftClip", "RightClip", "Flags", "IsSec", "IsSup", "ReadSeq", "ReadAlnSeq", "LeftSoftClipSeq", "RightSoftClip", "LeftHardClip", "RightHardClip"}
+	validFields := []string{"Read", "Ref", "Pos", "EndPos", "MapQual", "Acc", "Match", "Mismatch", "Ins", "Del", "AlnLen", "ReadLen", "RefLen", "RefAln", "RefCov", "ReadAln", "ReadCov", "Strand", "MeanQual", "LeftClip", "RightClip", "Flags", "IsSec", "IsSup", "ReadSeq", "ReadAlnSeq", "LeftSoftClipSeq", "RightSoftClipSeq", "RightSoftClip", "LeftHardClip", "RightHardClip"}
 
 	tsvFh := os.Stderr
 	tsvFile, err := p.Yaml.Get("Tsv").String()


=====================================
seqkit/cmd/grep.go
=====================================
@@ -46,17 +46,26 @@ var grepCmd = &cobra.Command{
 	Long: fmt.Sprintf(`search sequences by ID/name/sequence/sequence motifs, mismatch allowed
 
 Attentions:
+
   0. By default, we match sequence ID with patterns, use "-n/--by-name"
      for matching full name instead of just ID.
   1. Unlike POSIX/GNU grep, we compare the pattern to the whole target
      (ID/full header) by default. Please switch "-r/--use-regexp" on
      for partly matching.
-  2. While when searching by sequences, only positive strand is searched,
-     and it's partly matching. 
+  2. When searching by sequences, it's partly matching, and both positive
+     and negative strands are searched.
      Mismatch is allowed using flag "-m/--max-mismatch",
      but it's not fast enough for large genome like human genome.
      Though, it's fast enough for microbial genomes.
-  3. The order of sequences in result is consistent with that in original
+  3. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
+     But do not use degenerate bases/residues in regular expression, you need
+     convert them to regular expression, e.g., change "N" or "X"  to "."..
+  4. When providing search patterns (motifs) via flag '-p',
+     please use double quotation marks for patterns containing comma, 
+     e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
+     parser accepts comma-separated-values (CSV) for multiple values (motifs).
+     Patterns in file do not follow this rule.
+  5. The order of sequences in result is consistent with that in original
      file, not the order of the query patterns. 
      But for FASTA file, you can use:
         seqkit faidx seqs.fasta --infile-list IDs.txt
@@ -88,6 +97,7 @@ Examples:
 		deleteMatched := getFlagBool(cmd, "delete-matched")
 		invertMatch := getFlagBool(cmd, "invert-match")
 		bySeq := getFlagBool(cmd, "by-seq")
+		onlyPositiveStrand := getFlagBool(cmd, "only-positive-strand")
 		mismatches := getFlagNonNegativeInt(cmd, "max-mismatch")
 		byName := getFlagBool(cmd, "by-name")
 		ignoreCase := getFlagBool(cmd, "ignore-case")
@@ -256,6 +266,7 @@ Examples:
 		checkError(err)
 		defer outfh.Close()
 
+		var sequence *seq.Seq
 		var target []byte
 		var ok, hit bool
 		var record *fastx.Record
@@ -264,6 +275,8 @@ Examples:
 		var locs []int
 		var re *regexp.Regexp
 		var p string
+		strands := []byte{'+', '-'}
+		var strand byte
 		for _, file := range files {
 			fastxReader, err = fastx.NewReader(alphabet, file, idRegexp)
 			checkError(err)
@@ -285,76 +298,101 @@ Examples:
 				if byName {
 					target = record.Name
 				} else if bySeq {
-					if limitRegion {
-						target = record.Seq.SubSeq(start, end).Seq
-					} else if circular {
-						// concat two copies of sequence, and do not change orginal sequence
-						target = make([]byte, len(record.Seq.Seq)*2)
-						copy(target[0:len(record.Seq.Seq)], record.Seq.Seq)
-						copy(target[len(record.Seq.Seq):], record.Seq.Seq)
-					} else {
-						target = record.Seq.Seq
-					}
+
 				} else {
 					target = record.ID
 				}
 
 				hit = false
 
-				if degenerate || useRegexp {
-					for p, re = range patterns {
-						if re.Match(target) {
-							hit = true
-							if deleteMatched && !invertMatch {
-								delete(patterns, p)
+				for _, strand = range strands {
+					if hit {
+						break
+					}
+
+					if strand == '-' {
+						if bySeq {
+							if onlyPositiveStrand {
+								break
 							}
+						} else {
 							break
 						}
 					}
-				} else if bySeq {
-					if ignoreCase {
-						target = bytes.ToLower(target)
+
+					if bySeq {
+						sequence = record.Seq
+						if strand == '-' {
+							sequence = record.Seq.RevCom()
+						}
+						if limitRegion {
+							target = sequence.SubSeq(start, end).Seq
+						} else if circular {
+							// concat two copies of sequence, and do not change orginal sequence
+							target = make([]byte, len(sequence.Seq)*2)
+							copy(target[0:len(sequence.Seq)], sequence.Seq)
+							copy(target[len(sequence.Seq):], sequence.Seq)
+						} else {
+							target = sequence.Seq
+						}
 					}
-					if mismatches == 0 {
-						for k = range patterns {
-							if bytes.Contains(target, []byte(k)) {
+
+					if degenerate || useRegexp {
+						for p, re = range patterns {
+							if re.Match(target) {
 								hit = true
 								if deleteMatched && !invertMatch {
-									delete(patterns, k)
+									delete(patterns, p)
 								}
 								break
 							}
 						}
-					} else {
-						_, err = sfmi.Transform(target)
-						if err != nil {
-							checkError(fmt.Errorf("fail to build FMIndex for sequence: %s", record.Name))
+					} else if bySeq {
+						if ignoreCase {
+							target = bytes.ToLower(target)
 						}
-						for k = range patterns {
-							locs, err = sfmi.Locate([]byte(k), mismatches)
+						if mismatches == 0 {
+							for k = range patterns {
+								if bytes.Contains(target, []byte(k)) {
+									hit = true
+									if deleteMatched && !invertMatch {
+										delete(patterns, k)
+									}
+									break
+								}
+							}
+						} else {
+							_, err = sfmi.Transform(target)
 							if err != nil {
-								checkError(fmt.Errorf("fail to search pattern '%s' on seq '%s': %s", k, record.Name, err))
+								checkError(fmt.Errorf("fail to build FMIndex for sequence: %s", record.Name))
 							}
-							if len(locs) > 0 {
-								hit = true
-								if deleteMatched && !invertMatch {
-									delete(patterns, k)
+							for k = range patterns {
+								locs, err = sfmi.Locate([]byte(k), mismatches)
+								if err != nil {
+									checkError(fmt.Errorf("fail to search pattern '%s' on seq '%s': %s", k, record.Name, err))
+								}
+								if len(locs) > 0 {
+									hit = true
+									if deleteMatched && !invertMatch {
+										delete(patterns, k)
+									}
+									break
 								}
-								break
 							}
 						}
-					}
-				} else {
-					k = string(target)
-					if ignoreCase {
-						k = strings.ToLower(k)
-					}
-					if _, ok = patterns[k]; ok {
-						hit = true
-						if deleteMatched && !invertMatch {
-							delete(patterns, k)
+					} else {
+						k = string(target)
+						if ignoreCase {
+							k = strings.ToLower(k)
+						}
+						if _, ok = patterns[k]; ok {
+							hit = true
+							if deleteMatched && !invertMatch {
+								delete(patterns, k)
+							}
 						}
 					}
+
 				}
 
 				if invertMatch {
@@ -384,7 +422,8 @@ func init() {
 	grepCmd.Flags().BoolP("delete-matched", "", false, "delete a pattern right after being matched, this keeps the firstly matched data and speedups when using regular expressions")
 	grepCmd.Flags().BoolP("invert-match", "v", false, "invert the sense of matching, to select non-matching records")
 	grepCmd.Flags().BoolP("by-name", "n", false, "match by full name instead of just ID")
-	grepCmd.Flags().BoolP("by-seq", "s", false, "search subseq on seq, only positive strand is searched, and mismatch allowed using flag -m/--max-mismatch")
+	grepCmd.Flags().BoolP("by-seq", "s", false, "search subseq on seq, both positive and negative strand are searched, and mismatch allowed using flag -m/--max-mismatch")
+	grepCmd.Flags().BoolP("only-positive-strand", "P", false, "only search on positive strand")
 	grepCmd.Flags().IntP("max-mismatch", "m", 0, "max mismatch when matching by seq. For large genomes like human genome, using mapping/alignment tools would be faster")
 	grepCmd.Flags().BoolP("ignore-case", "i", false, "ignore case")
 	grepCmd.Flags().BoolP("degenerate", "d", false, "pattern/motif contains degenerate base")


=====================================
seqkit/cmd/locate.go
=====================================
@@ -41,20 +41,23 @@ var locateCmd = &cobra.Command{
 	Short: "locate subsequences/motifs, mismatch allowed",
 	Long: `locate subsequences/motifs, mismatch allowed
 
-Motifs could be EITHER plain sequence containing "ACTGN" OR regular
-expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.
-Degenerate bases like "RYMM.." are also supported by flag -d.
-
-By default, motifs are treated as regular expression.
-When flag -d given, regular expression may be wrong.
-For example: "\w" will be wrongly converted to "\[AT]".
-
-Mismatch is allowed using flag "-m/--max-mismatch",
-but it's not fast enough for large genome like human genome.
-Though, it's fast enough for microbial genomes.
-
-When using flag --circular, end position of matched subsequence that 
-crossing genome sequence end would be greater than sequence length.
+Attentions:
+
+  1. Motifs could be EITHER plain sequence containing "ACTGN" OR regular
+     expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.     
+  2. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
+     But do not use degenerate bases/residues in regular expression, you need
+     convert them to regular expression, e.g., change "N" or "X"  to "."..
+  3. When providing search patterns (motifs) via flag '-p',
+     please use double quotation marks for patterns containing comma, 
+     e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
+     parser accepts comma-separated-values (CSV) for multiple values (motifs).
+     Patterns in file do not follow this rule.     
+  4. Mismatch is allowed using flag "-m/--max-mismatch",
+     but it's not fast enough for large genome like human genome.
+     Though, it's fast enough for microbial genomes.
+  5. When using flag --circular, end position of matched subsequence that 
+     crossing genome sequence end would be greater than sequence length.
 
 `,
 	Run: func(cmd *cobra.Command, args []string) {
@@ -89,6 +92,10 @@ crossing genome sequence end would be greater than sequence length.
 		hideMatched := getFlagBool(cmd, "hide-matched")
 		circular := getFlagBool(cmd, "circular")
 
+		if config.Alphabet == seq.Protein {
+			onlyPositiveStrand = true
+		}
+
 		if len(pattern) == 0 && patternFile == "" {
 			checkError(fmt.Errorf("one of flags -p (--pattern) and -f (--pattern-file) needed"))
 		}
@@ -209,6 +216,7 @@ crossing genome sequence end would be greater than sequence length.
 						}
 						re, err := regexp.Compile(s)
 						checkError(err)
+						fmt.Println(s, re)
 						regexps[p] = re
 					} else if bytes.Index(patterns[p], []byte(".")) >= 0 ||
 						!(seq.DNAredundant.IsValid(patterns[p]) == nil ||


=====================================
seqkit/cmd/seq.go
=====================================
@@ -42,6 +42,10 @@ var seqCmd = &cobra.Command{
 	Short: "transform sequences (revserse, complement, extract ID...)",
 	Long: `transform sequences (revserse, complement, extract ID...)
 
+Attentions:
+
+  1. This command outputs plain text even when out file ends with ".gz".
+
 `,
 	Run: func(cmd *cobra.Command, args []string) {
 		config := getConfigs(cmd)


=====================================
seqkit/cmd/shuffle.go
=====================================
@@ -216,7 +216,6 @@ Secondly, seqkit shuffles sequence IDs and extract sequences by FASTA index.
 			sequence := subseqByFaixNotCleaned(faidx, chr, r, 1, -1)
 			outfh.Write([]byte(fmt.Sprintf(">%s\n", chr)))
 			outfh.Write(sequence)
-			outfh.WriteString("\n")
 		}
 
 		if (isStdin(file) || !isPlainFile(file)) && !keepTemp {


=====================================
seqkit/cmd/split2.go
=====================================
@@ -90,9 +90,13 @@ according to the input files.
 		force := getFlagBool(cmd, "force")
 
 		if size == 0 && parts == 0 && length == 0 {
-			checkError(fmt.Errorf(`one of flags should be given: -s/-p. type "seqkit split2 -h" for help`))
+			checkError(fmt.Errorf(`one of flags should be given: -s/-p/-l. type "seqkit split2 -h" for help`))
 		}
 
+		bySize := size > 0
+		byParts := parts > 0
+		byLength := length > 0
+
 		if parts >= 1000 {
 			log.Warningf(`value of -p/--parts > 1000 may cause error of "too many open files"`)
 		}
@@ -134,9 +138,9 @@ according to the input files.
 
 		if !quiet {
 			log.Infof("split seqs from %s", source)
-			if size > 0 {
+			if bySize {
 				log.Infof("split into %d seqs per file", size)
-			} else if parts > 0 {
+			} else if byParts {
 				log.Infof("split into %d parts", parts)
 			} else {
 				log.Infof("split by sequence length: %s", lengthS)
@@ -192,23 +196,24 @@ according to the input files.
 				var counts []int
 				var outfiles []string
 
-				if size > 0 || length > 0 { // by size or by length
+				var flag bool
+
+				if bySize || byLength { // by size or by length
 					outfhs = make([]*xopen.Writer, 0, 10)
 					counts = make([]int, 0, 10)
 					outfiles = make([]string, 0, 10)
-				} else if parts > 0 { // by part
+				} else if byParts { // by part
 					outfhs = make([]*xopen.Writer, 0, parts)
 					counts = make([]int, 0, parts)
 					outfiles = make([]string, 0, parts)
 				} else {
-					checkError(fmt.Errorf(`one of flags should be given: -s/-p. type "seqkit split2 -h" for help`))
+					checkError(fmt.Errorf(`one of flags should be given: -s/-p/-l. type "seqkit split2 -h" for help`))
 				}
 
-				var outfh *xopen.Writer
 				fastxReader, err = fastx.NewReader(alphabet, file, idRegexp)
 				checkError(err)
-				i := 0      // nth part
-				j := 0      // nth record
+				i := 0 // nth part
+				j := 0
 				var n int64 // length sum
 				for {
 					record, err = fastxReader.Read()
@@ -219,6 +224,7 @@ according to the input files.
 						checkError(err)
 						break
 					}
+
 					if fastxReader.IsFastq {
 						config.LineWidth = 0
 						fastx.ForcelyOutputFastq = true
@@ -234,7 +240,7 @@ according to the input files.
 					}
 					n += int64(len(record.Seq.Seq))
 
-					if size > 0 {
+					if bySize {
 						if j == size {
 							outfhs[i].Close()
 							if !quiet {
@@ -254,25 +260,55 @@ according to the input files.
 
 							j = 0
 						}
-					} else if length > 0 {
+					} else if byLength {
+						flag = false
 						if n >= length {
-							outfhs[i].Close()
-							if !quiet {
-								log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
+							if len(outfhs) == 0 { // order is different
+								var outfh2 *xopen.Writer
+								outfile := filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i+1, fileExt))
+								outfh2, err = xopen.Wopen(outfile)
+								checkError(err)
+
+								outfhs = append(outfhs, outfh2)
+								counts = append(counts, 0)
+								outfiles = append(outfiles, outfile)
+
+								record.FormatToWriter(outfhs[i], config.LineWidth)
+								counts[i]++
+
+								outfhs[i].Close()
+								if !quiet {
+									log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
+								}
+								outfhs[i] = nil
+								i++
+
+								n = 0
+							} else {
+								record.FormatToWriter(outfhs[i], config.LineWidth)
+								counts[i]++
+
+								outfhs[i].Close()
+								if !quiet {
+									log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
+								}
+								outfhs[i] = nil
+								i++
+
+								var outfh2 *xopen.Writer
+								outfile := filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i+1, fileExt))
+								outfh2, err = xopen.Wopen(outfile)
+								checkError(err)
+
+								outfhs = append(outfhs, outfh2)
+								counts = append(counts, 0)
+								outfiles = append(outfiles, outfile)
+
+								n = 0
 							}
-							outfhs[i] = nil
-
-							i++
-							var outfh2 *xopen.Writer
-							outfile := filepath.Join(outdir, fmt.Sprintf("%s.part_%03d%s", filepath.Base(fileName), i+1, fileExt))
-							outfh2, err = xopen.Wopen(outfile)
-							checkError(err)
-
-							outfhs = append(outfhs, outfh2)
-							counts = append(counts, 0)
-							outfiles = append(outfiles, outfile)
-
-							n = 0
+							flag = false
+						} else { // write this record later
+							flag = true
 						}
 					}
 
@@ -286,15 +322,20 @@ according to the input files.
 						counts = append(counts, 0)
 						outfiles = append(outfiles, outfile)
 					}
-					outfh = outfhs[i]
 
-					record.FormatToWriter(outfh, config.LineWidth)
-
-					counts[i]++
+					if byLength {
+						if flag {
+							record.FormatToWriter(outfhs[i], config.LineWidth)
+							counts[i]++
+						}
+					} else {
+						record.FormatToWriter(outfhs[i], config.LineWidth)
+						counts[i]++
+					}
 
-					if size > 0 {
+					if bySize {
 						j++ // increase size
-					} else if parts > 0 {
+					} else if byParts {
 						i++
 						if i == parts { // reset index
 							i = 0
@@ -304,15 +345,20 @@ according to the input files.
 					}
 				}
 
-				// for by-size/length: only log last part,
+				// for by-size: only log last part,
 				// for by-parts: log all parts.
 				for i, outfh := range outfhs {
-					if outfh != nil {
-						outfh.Close()
+					if outfh == nil {
+						continue
 					}
+					outfh.Close()
 
 					if !quiet {
-						log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
+						if counts[i] == 0 {
+							os.Remove(outfiles[i])
+						} else {
+							log.Infof("write %d sequences to file: %s\n", counts[i], outfiles[i])
+						}
 					}
 				}
 
@@ -330,7 +376,7 @@ func init() {
 	split2Cmd.Flags().StringP("read2", "2", "", "(gzipped) read2 file")
 	split2Cmd.Flags().IntP("by-size", "s", 0, "split sequences into multi parts with N sequences")
 	split2Cmd.Flags().IntP("by-part", "p", 0, "split sequences into N parts")
-	split2Cmd.Flags().StringP("by-length", "l", "", "split sequences into chunks of N bases, supports K/M/G suffix")
+	split2Cmd.Flags().StringP("by-length", "l", "", "split sequences into chunks of >=N bases, supports K/M/G suffix")
 	split2Cmd.Flags().StringP("out-dir", "O", "", "output directory (default value is $infile.split)")
 	split2Cmd.Flags().BoolP("force", "f", false, "overwrite output directory")
 }


=====================================
seqkit/cmd/version.go
=====================================
@@ -29,7 +29,7 @@ import (
 )
 
 // VERSION of seqkit
-const VERSION = "0.14.0"
+const VERSION = "0.15.0"
 
 // versionCmd represents the version command
 var versionCmd = &cobra.Command{


=====================================
seqkit/packaging.sh
=====================================
@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-CGO_ENABLED=0 gox -os="windows darwin linux" -arch="386 amd64" -tags netgo -ldflags '-w -s' -asmflags '-trimpath'
+CGO_ENABLED=0 gox -os="windows darwin linux" -arch="386 amd64 arm64" -tags netgo -ldflags '-w -s' -asmflags '-trimpath'
 
 dir=binaries
 mkdir -p $dir;


=====================================
tests/test.sh
=====================================
@@ -605,7 +605,7 @@ fun(){
 	SCAT_PID=$!
         BAK=$IFS
         IFS=$'\n'
-	SIZE=3
+	SIZE=2
         for i in `seq 0 $SIZE`;
         do
                 for j in `seq 0 $SIZE`;
@@ -652,7 +652,7 @@ fun(){
 	SCAT_PID=$!
         BAK=$IFS
         IFS=$'\n'
-	SIZE=3
+	SIZE=2
         for i in `seq 0 $SIZE`;
         do
                 for j in `seq 0 $SIZE`;



View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/commit/8fdd687f430dbc8efa4d31b6edfb001a81db3a12

-- 
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/commit/8fdd687f430dbc8efa4d31b6edfb001a81db3a12
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