[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)
+[](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)
[](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)
-[](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)
+[](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) |[](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) |[](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) |[](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) |[](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) |[](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)|[](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) |[](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) |[](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) |[](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) |[](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) |[](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) |[](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)|[](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)
+[](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)
[](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
=====================================
@@ -0,0 +1,386 @@
+cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
+cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw=
+cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU=
+cloud.google.com/go v0.44.1/go.mod h1:iSa0KzasP4Uvy3f1mN/7PiObzGgflwredwwASm/v6AU=
+cloud.google.com/go v0.44.2/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY=
+cloud.google.com/go v0.45.1/go.mod h1:RpBamKRgapWJb87xiFSdk4g1CME7QZg3uwTez+TSTjc=
+cloud.google.com/go v0.46.3/go.mod h1:a6bKKbmY7er1mI7TEI4lsAkts/mkhTSZK8w33B4RAg0=
+cloud.google.com/go/bigquery v1.0.1/go.mod h1:i/xbL2UlR5RvWAURpBYZTtm/cXjCha9lbfbpx4poX+o=
+cloud.google.com/go/datastore v1.0.0/go.mod h1:LXYbyblFSglQ5pkeyhO+Qmw7ukd3C+pD7TKLgZqpHYE=
+cloud.google.com/go/firestore v1.1.0/go.mod h1:ulACoGHTpvq5r8rxGJ4ddJZBZqakUQqClKRT5SZwBmk=
+cloud.google.com/go/pubsub v1.0.1/go.mod h1:R0Gpsv3s54REJCy4fxDixWD93lHJMoZTyQ2kNxGRt3I=
+cloud.google.com/go/storage v1.0.0/go.mod h1:IhtSnM/ZTZV8YYJWCY8RULGVqBDmpoyjwiyrjsg+URw=
+dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU=
+github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU=
+github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo=
+github.com/OneOfOne/xxhash v1.2.2 h1:KMrpdQIwFcEqXDklaen+P1axHaj9BSKzvpUUfnHldSE=
+github.com/OneOfOne/xxhash v1.2.2/go.mod h1:HSdplMjZKSmBqAxg5vPj2TmRDmfkzw+cTzAElWljhcU=
+github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af h1:wVe6/Ea46ZMeNkQjjBW6xcqyQA/j5e0D6GytH95g0gQ=
+github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af/go.mod h1:K08gAheRH3/J6wwsYMMT4xOr94bZjxIelGM0+d/wbFw=
+github.com/alecthomas/template v0.0.0-20160405071501-a0175ee3bccc/go.mod h1:LOuyumcjzFXgccqObfd/Ljyb9UuFJ6TxHnclSeseNhc=
+github.com/alecthomas/units v0.0.0-20151022065526-2efee857e7cf/go.mod h1:ybxpYRFXyAe+OPACYpWeL0wqObRcbAqCMya13uyzqw0=
+github.com/armon/circbuf v0.0.0-20150827004946-bbbad097214e/go.mod h1:3U/XgcO3hCbHZ8TKRvWD2dDTCfh9M9ya+I9JpbB7O8o=
+github.com/armon/go-metrics v0.0.0-20180917152333-f0300d1749da/go.mod h1:Q73ZrmVTwzkszR9V5SSuryQ31EELlFMUz1kKyl939pY=
+github.com/armon/go-radix v0.0.0-20180808171621-7fddfc383310/go.mod h1:ufUuZ+zHj4x4TnLV4JWEpy2hxWSpsRywHrMgIH9cCH8=
+github.com/beorn7/perks v0.0.0-20180321164747-3a771d992973/go.mod h1:Dwedo/Wpr24TaqPxmxbtue+5NUziq4I4S80YR8gNf3Q=
+github.com/beorn7/perks v1.0.0/go.mod h1:KWe93zE9D1o94FZ5RNwFwVgaQK1VOXiVxmqh+CedLV8=
+github.com/bgentry/speakeasy v0.1.0/go.mod h1:+zsyZBPWlz7T6j88CTgSN5bM796AkVf0kBD4zp0CCIs=
+github.com/biogo/biogo v1.0.3 h1:LSRUaHBW5WyyTBkfG9lGZOych6uvfbFPB9j9OLaZ7Nw=
+github.com/biogo/biogo v1.0.3/go.mod h1:WlqzR+oIOt6UKRqDbDsbLm7zHe4+FLLDd9iFTrnfloc=
+github.com/biogo/boom v0.0.0-20150317015657-28119bc1ffc1 h1:LAHY5JxqhOgJDeDBGKsQ4300qd3sG8C0j5CQS8gD+Kw=
+github.com/biogo/boom v0.0.0-20150317015657-28119bc1ffc1/go.mod h1:fwtxkutinkQcME9Zlywh66T0jZLLjgrwSLY2WxH2N3U=
+github.com/biogo/graph v0.0.0-20150317020928-057c1989faed/go.mod h1:UuyD2swDzTz1ChZTQld42mP5pyePLSDccmGycTpxRew=
+github.com/biogo/hts v1.1.0/go.mod h1:6C9MdMt9ALD5PsluK5n0B0svHOpmVse3UjQQx/cTgOw=
+github.com/biogo/hts v1.2.2 h1:n+o6v+oWMfPR4oksDJndEDxgL7ee53Pltn7V9PxqXzc=
+github.com/biogo/hts v1.2.2/go.mod h1:6C9MdMt9ALD5PsluK5n0B0svHOpmVse3UjQQx/cTgOw=
+github.com/biogo/store v0.0.0-20200104231603-2c6ad937eb83/go.mod h1:wdbXg77soR6ESRprAMEwAQDFtLT6EAGF5o1GRy0cB5k=
+github.com/bketelsen/crypt v0.0.3-0.20200106085610-5cbc8cc4026c/go.mod h1:MKsuJmJgSg28kpZDP6UIiPt0e0Oz0kqKNGyRaWEPv84=
+github.com/bsipos/thist v1.0.0 h1:vZ3W5/ZnT54s4LHeonTCbnzCb20ERlJUnhiwXoGpsbY=
+github.com/bsipos/thist v1.0.0/go.mod h1:7i0xwRua1/bmUxcxi2xAxaFL895rLtOpKUwnw3NrT8I=
+github.com/cespare/xxhash v1.1.0 h1:a6HrQnmkObjyL+Gs60czilIUGqrzKutQD6XZog3p+ko=
+github.com/cespare/xxhash v1.1.0/go.mod h1:XrSqR1VqqWfGrhpAt58auRo0WTKS1nRRg3ghfAqPWnc=
+github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw=
+github.com/coreos/bbolt v1.3.2/go.mod h1:iRUV2dpdMOn7Bo10OQBFzIJO9kkE559Wcmn+qkEiiKk=
+github.com/coreos/etcd v3.3.13+incompatible/go.mod h1:uF7uidLiAD3TWHmW31ZFd/JWoc32PjwdhPthX9715RE=
+github.com/coreos/go-semver v0.3.0/go.mod h1:nnelYz7RCh+5ahJtPPxZlU+153eP4D4r3EedlOD2RNk=
+github.com/coreos/go-systemd v0.0.0-20190321100706-95778dfbb74e/go.mod h1:F5haX7vjVVG0kc13fIWeqUViNPyEJxv/OmvnBo0Yme4=
+github.com/coreos/pkg v0.0.0-20180928190104-399ea9e2e55f/go.mod h1:E3G3o1h8I7cfcXa63jLwjI0eiQQMgzzUDFVpN/nH/eA=
+github.com/cpuguy83/go-md2man/v2 v2.0.0/go.mod h1:maD7wRr/U5Z6m/iR4s+kqSMx2CaBsrgA7czyZG/E6dU=
+github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548 h1:iwZdTE0PVqJCos1vaoKsclOGD3ADKpshg3SRtYBbwso=
+github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548/go.mod h1:e6NPNENfs9mPDVNRekM7lKScauxd5kXTr1Mfyig6TDM=
+github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8 h1:LpMLYGyy67BoAFGda1NeOBQwqlv7nUXpm+rIVHGxZZ4=
+github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8/go.mod h1:q2w6Bg5jeox1B+QkJ6Wp/+Vn0G/bo3f1uY7Fn3vivIQ=
+github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/dgrijalva/jwt-go v3.2.0+incompatible/go.mod h1:E3ru+11k8xSBh+hMPgOLZmtrrCbhqsmaPHjLKYnJCaQ=
+github.com/dgryski/go-sip13 v0.0.0-20181026042036-e10d5fee7954/go.mod h1:vAd38F8PWV+bWy6jNmig1y/TA+kYO4g3RSRF0IAv0no=
+github.com/dustin/go-humanize v1.0.0 h1:VSnTsYCnlFHaM2/igO1h6X3HA71jcobQuxemgkq4zYo=
+github.com/dustin/go-humanize v1.0.0/go.mod h1:HtrtbFcZ19U5GC7JDqmcUSB87Iq5E25KnS6fMYU6eOk=
+github.com/edsrzf/mmap-go v1.0.0 h1:CEBF7HpRnUCSJgGUb5h1Gm7e3VkmVDrR8lvWVLtrOFw=
+github.com/edsrzf/mmap-go v1.0.0/go.mod h1:YO35OhQPt3KJa3ryjFM5Bs14WD66h8eGKpfaBNrHW5M=
+github.com/fatih/color v1.7.0/go.mod h1:Zm6kSWBoL9eyXnKyktHP6abPY2pDugNf5KwzbycvMj4=
+github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90 h1:WXb3TSNmHp2vHoCroCIB1foO/yQ36swABL8aOVeDpgg=
+github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90/go.mod h1:R/bRT+9gY/C5z7JzPU0zXsXHKM4/ayA+zqcVNZzPa1k=
+github.com/fsnotify/fsnotify v1.4.7/go.mod h1:jwhsz4b93w/PPRr/qN1Yymfu8t87LnFCMoQvtojpjFo=
+github.com/fsnotify/fsnotify v1.4.9 h1:hsms1Qyu0jgnwNXIxa+/V/PDsU6CfLf6CNO8H7IWoS4=
+github.com/fsnotify/fsnotify v1.4.9/go.mod h1:znqG4EE+3YCdAaPaxE2ZRY/06pZUdp0tY4IgpuI1SZQ=
+github.com/ghodss/yaml v1.0.0/go.mod h1:4dBDuWmgqj2HViK6kFavaiC9ZROes6MMH2rRYeMEF04=
+github.com/go-gl/glfw v0.0.0-20190409004039-e6da0acd62b1/go.mod h1:vR7hzQXu2zJy9AVAgeJqvqgH9Q5CA+iKCZ2gyEVpxRU=
+github.com/go-gl/glfw/v3.3/glfw v0.0.0-20191125211704-12ad95a8df72/go.mod h1:tQ2UAYgL5IevRw8kRxooKSPJfGvJ9fJQFa0TUsXzTg8=
+github.com/go-kit/kit v0.8.0/go.mod h1:xBxKIO96dXMWWy0MnWVtmwkA9/13aqxPnvrjFYMA2as=
+github.com/go-logfmt/logfmt v0.3.0/go.mod h1:Qt1PoO58o5twSAckw1HlFXLmHsOX5/0LbT9GBnD5lWE=
+github.com/go-logfmt/logfmt v0.4.0/go.mod h1:3RMwSq7FuexP4Kalkev3ejPJsZTpXXBr9+V4qmtdjCk=
+github.com/go-stack/stack v1.8.0/go.mod h1:v0f6uXyyMGvRgIKkXu+yp6POWl0qKG85gN/melR3HDY=
+github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ=
+github.com/gogo/protobuf v1.2.1/go.mod h1:hp+jE20tsWTFYpLwKvXlhS1hjn+gTNwPg2I6zVXpSg4=
+github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0 h1:DACJavvAHhabrF08vX0COfcOBJRhZ8lUbR+ZWIs0Y5g=
+github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0/go.mod h1:E/TSTwGwJL78qG/PmXZO1EjYhfJinVAhrmmHX6Z8B9k=
+github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q=
+github.com/golang/groupcache v0.0.0-20190129154638-5b532d6fd5ef/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc=
+github.com/golang/mock v1.1.1/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A=
+github.com/golang/mock v1.2.0/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A=
+github.com/golang/mock v1.3.1/go.mod h1:sBzyDLLjw3U8JLTeZvSv8jJB+tU5PVekmnlKIyFUx0Y=
+github.com/golang/protobuf v1.2.0/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
+github.com/golang/protobuf v1.3.1/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
+github.com/golang/protobuf v1.3.2/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U=
+github.com/google/btree v0.0.0-20180813153112-4030bb1f1f0c/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ=
+github.com/google/btree v1.0.0/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ=
+github.com/google/go-cmp v0.2.0/go.mod h1:oXzfMopK8JAjlY9xF4vHSVASa0yLyX7SntLO5aqRK0M=
+github.com/google/go-cmp v0.3.0/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU=
+github.com/google/martian v2.1.0+incompatible/go.mod h1:9I4somxYTbIHy5NJKHRl3wXiIaQGbYVAs8BPL6v8lEs=
+github.com/google/pprof v0.0.0-20181206194817-3ea8567a2e57/go.mod h1:zfwlbNMJ+OItoe0UupaVj+oy1omPYYDuagoSzA8v9mc=
+github.com/google/pprof v0.0.0-20190515194954-54271f7e092f/go.mod h1:zfwlbNMJ+OItoe0UupaVj+oy1omPYYDuagoSzA8v9mc=
+github.com/google/renameio v0.1.0/go.mod h1:KWCgfxg9yswjAJkECMjeO8J8rahYeXnNhOm40UhjYkI=
+github.com/googleapis/gax-go/v2 v2.0.4/go.mod h1:0Wqv26UfaUD9n4G6kQubkQ+KchISgw+vpHVxEJEs9eg=
+github.com/googleapis/gax-go/v2 v2.0.5/go.mod h1:DWXyrwAJ9X0FpwwEdw+IPEYBICEFu5mhpdKc/us6bOk=
+github.com/gopherjs/gopherjs v0.0.0-20181017120253-0766667cb4d1/go.mod h1:wJfORRmW1u3UXTncJ5qlYoELFm8eSnnEO6hX4iZ3EWY=
+github.com/gorilla/websocket v1.4.2/go.mod h1:YR8l580nyteQvAITg2hZ9XVh4b55+EU/adAjf1fMHhE=
+github.com/grpc-ecosystem/go-grpc-middleware v1.0.0/go.mod h1:FiyG127CGDf3tlThmgyCl78X/SZQqEOJBCDaAfeWzPs=
+github.com/grpc-ecosystem/go-grpc-prometheus v1.2.0/go.mod h1:8NvIoxWQoOIhqOTXgfV/d3M/q6VIi02HzZEHgUlZvzk=
+github.com/grpc-ecosystem/grpc-gateway v1.9.0/go.mod h1:vNeuVxBJEsws4ogUvrchl83t/GYV9WGTSLVdBhOQFDY=
+github.com/hashicorp/consul/api v1.1.0/go.mod h1:VmuI/Lkw1nC05EYQWNKwWGbkg+FbDBtguAZLlVdkD9Q=
+github.com/hashicorp/consul/sdk v0.1.1/go.mod h1:VKf9jXwCTEY1QZP2MOLRhb5i/I/ssyNV1vwHyQBF0x8=
+github.com/hashicorp/errwrap v1.0.0/go.mod h1:YH+1FKiLXxHSkmPseP+kNlulaMuP3n2brvKWEqk/Jc4=
+github.com/hashicorp/go-cleanhttp v0.5.1/go.mod h1:JpRdi6/HCYpAwUzNwuwqhbovhLtngrth3wmdIIUrZ80=
+github.com/hashicorp/go-immutable-radix v1.0.0/go.mod h1:0y9vanUI8NX6FsYoO3zeMjhV/C5i9g4Q3DwcSNZ4P60=
+github.com/hashicorp/go-msgpack v0.5.3/go.mod h1:ahLV/dePpqEmjfWmKiqvPkv/twdG7iPBM1vqhUKIvfM=
+github.com/hashicorp/go-multierror v1.0.0/go.mod h1:dHtQlpGsu+cZNNAkkCN/P3hoUDHhCYQXV3UM06sGGrk=
+github.com/hashicorp/go-rootcerts v1.0.0/go.mod h1:K6zTfqpRlCUIjkwsN4Z+hiSfzSTQa6eBIzfwKfwNnHU=
+github.com/hashicorp/go-sockaddr v1.0.0/go.mod h1:7Xibr9yA9JjQq1JpNB2Vw7kxv8xerXegt+ozgdvDeDU=
+github.com/hashicorp/go-syslog v1.0.0/go.mod h1:qPfqrKkXGihmCqbJM2mZgkZGvKG1dFdvsLplgctolz4=
+github.com/hashicorp/go-uuid v1.0.0/go.mod h1:6SBZvOh/SIDV7/2o3Jml5SYk/TvGqwFJ/bN7x4byOro=
+github.com/hashicorp/go-uuid v1.0.1/go.mod h1:6SBZvOh/SIDV7/2o3Jml5SYk/TvGqwFJ/bN7x4byOro=
+github.com/hashicorp/go.net v0.0.1/go.mod h1:hjKkEWcCURg++eb33jQU7oqQcI9XDCnUzHA0oac0k90=
+github.com/hashicorp/golang-lru v0.5.0/go.mod h1:/m3WP610KZHVQ1SGc6re/UDhFvYD7pJ4Ao+sR/qLZy8=
+github.com/hashicorp/golang-lru v0.5.1/go.mod h1:/m3WP610KZHVQ1SGc6re/UDhFvYD7pJ4Ao+sR/qLZy8=
+github.com/hashicorp/hcl v1.0.0/go.mod h1:E5yfLk+7swimpb2L/Alb/PJmXilQ/rhwaUYs4T20WEQ=
+github.com/hashicorp/logutils v1.0.0/go.mod h1:QIAnNjmIWmVIIkWDTG1z5v++HQmx9WQRO+LraFDTW64=
+github.com/hashicorp/mdns v1.0.0/go.mod h1:tL+uN++7HEJ6SQLQ2/p+z2pH24WQKWjBPkE0mNTz8vQ=
+github.com/hashicorp/memberlist v0.1.3/go.mod h1:ajVTdAv/9Im8oMAAj5G31PhhMCZJV2pPBoIllUwCN7I=
+github.com/hashicorp/serf v0.8.2/go.mod h1:6hOLApaqBFA1NXqRQAsxw9QxuDEvNxSQRwA/JwenrHc=
+github.com/iafan/cwalk v0.0.0-20191125092548-dd7f505d2f66 h1:nC48Zi9jZpiu0QZkqMpmKpG2J3ytdSW5WKcm8ON0T0g=
+github.com/iafan/cwalk v0.0.0-20191125092548-dd7f505d2f66/go.mod h1:qVux82tax0171OVITiCxp2fPNmpP4jv3/RHLcqZ0Pf4=
+github.com/inconshreveable/mousetrap v1.0.0 h1:Z8tu5sraLXCXIcARxBp/8cbvlwVa7Z1NHg9XEKhtSvM=
+github.com/inconshreveable/mousetrap v1.0.0/go.mod h1:PxqpIevigyE2G7u3NXJIT2ANytuPF1OarO4DADm73n8=
+github.com/jonboulle/clockwork v0.1.0/go.mod h1:Ii8DK3G1RaLaWxj9trq07+26W01tbo22gdxWY5EU2bo=
+github.com/json-iterator/go v1.1.6/go.mod h1:+SdeFBvtyEkXs7REEP0seUULqWtbJapLOCVDaaPEHmU=
+github.com/jstemmer/go-junit-report v0.0.0-20190106144839-af01ea7f8024/go.mod h1:6v2b51hI/fHJwM22ozAgKL4VKDeJcHhJFhtBdhmNjmU=
+github.com/jtolds/gls v4.20.0+incompatible/go.mod h1:QJZ7F/aHp+rZTRtaJ1ow/lLfFfVYBRgL+9YlvaHOwJU=
+github.com/julienschmidt/httprouter v1.2.0/go.mod h1:SYymIcj16QtmaHHD7aYtjjsJG7VTCxuUUipMqKk8s4w=
+github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5 h1:PJr+ZMXIecYc1Ey2zucXdR73SMBtgjPgwa31099IMv0=
+github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5/go.mod h1:7Id9E/uU8ce6rXgefFLlgrJj/GYY22cpxn+r32jIOes=
+github.com/kisielk/errcheck v1.1.0/go.mod h1:EZBBE59ingxPouuu3KfxchcWSUPOHkagtvWXihfKN4Q=
+github.com/kisielk/gotool v1.0.0/go.mod h1:XhKaO+MFFWcvkIS/tQcRk01m1F5IRFswLeQ+oQHNcck=
+github.com/klauspost/compress v1.11.4 h1:kz40R/YWls3iqT9zX9AHN3WoVsrAWVyui5sxuLqiXqU=
+github.com/klauspost/compress v1.11.4/go.mod h1:aoV0uJVorq1K+umq18yTdKaF57EivdYsUV+/s2qKfXs=
+github.com/klauspost/pgzip v1.2.5 h1:qnWYvvKqedOF2ulHpMG72XQol4ILEJ8k2wwRl/Km8oE=
+github.com/klauspost/pgzip v1.2.5/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs=
+github.com/konsorten/go-windows-terminal-sequences v1.0.1/go.mod h1:T0+1ngSBFLxvqU3pZ+m/2kptfBszLMUkC4ZK/EgS/cQ=
+github.com/kortschak/utter v0.0.0-20190412033250-50fe362e6560/go.mod h1:oDr41C7kH9wvAikWyFhr6UFr8R7nelpmCF5XR5rL7I8=
+github.com/kr/logfmt v0.0.0-20140226030751-b84e30acd515/go.mod h1:+0opPa2QZZtGFBFZlji/RkVcI2GknAs/DXo4wKdlNEc=
+github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo=
+github.com/kr/pretty v0.2.0 h1:s5hAObm+yFO5uHYt5dYjxi2rXrsnmRpJx4OYvIWUaQs=
+github.com/kr/pretty v0.2.0/go.mod h1:ipq/a2n7PKx3OHsz4KJII5eveXtPO4qwEXGdVfWzfnI=
+github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ=
+github.com/kr/text v0.1.0 h1:45sCR5RtlFHMR4UwH9sdQ5TC8v0qDQCHnXt+kaKSTVE=
+github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI=
+github.com/logrusorgru/aurora v2.0.3+incompatible h1:tOpm7WcpBTn4fjmVfgpQq0EfczGlG91VSDkswnjF5A8=
+github.com/logrusorgru/aurora v2.0.3+incompatible/go.mod h1:7rIyQOR62GCctdiQpZ/zOJlFyk6y+94wXzv6RNZgaR4=
+github.com/magiconair/properties v1.8.1/go.mod h1:PppfXfuXeibc/6YijjN8zIbojt8czPbwD3XqdrwzmxQ=
+github.com/mattn/go-colorable v0.0.9/go.mod h1:9vuHe8Xs5qXnSaW/c/ABM9alt+Vo+STaOChaDxuIBZU=
+github.com/mattn/go-colorable v0.1.8 h1:c1ghPdyEDarC70ftn0y+A/Ee++9zz8ljHG1b13eJ0s8=
+github.com/mattn/go-colorable v0.1.8/go.mod h1:u6P/XSegPjTcexA+o6vUJrdnUu04hMope9wVRipJSqc=
+github.com/mattn/go-isatty v0.0.3/go.mod h1:M+lRXTBqGeGNdLjl/ufCoiOlB5xdOkqRJdNxMWT7Zi4=
+github.com/mattn/go-isatty v0.0.12 h1:wuysRhFDzyxgEmMf5xjvJ2M9dZoWAXNNr5LSBS7uHXY=
+github.com/mattn/go-isatty v0.0.12/go.mod h1:cbi8OIDigv2wuxKPP5vlRcQ1OAZbq2CE4Kysco4FUpU=
+github.com/mattn/go-runewidth v0.0.9 h1:Lm995f3rfxdpd6TSmuVCHVb/QhupuXlYr8sCI/QdE+0=
+github.com/mattn/go-runewidth v0.0.9/go.mod h1:H031xJmbD/WCDINGzjvQ9THkh0rPKHF+m2gUSrubnMI=
+github.com/matttproud/golang_protobuf_extensions v1.0.1/go.mod h1:D8He9yQNgCq6Z5Ld7szi9bcBfOoFv/3dc6xSMkL2PC0=
+github.com/miekg/dns v1.0.14/go.mod h1:W1PPwlIAgtquWBMBEV9nkV9Cazfe8ScdGz/Lj7v3Nrg=
+github.com/mitchellh/cli v1.0.0/go.mod h1:hNIlj7HEI86fIcpObd7a0FcrxTWetlwJDGcceTlRvqc=
+github.com/mitchellh/go-homedir v1.0.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrkLzIz1N1q0pr0=
+github.com/mitchellh/go-homedir v1.1.0 h1:lukF9ziXFxDFPkA1vsr5zpc1XuPDn/wFntq5mG+4E0Y=
+github.com/mitchellh/go-homedir v1.1.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrkLzIz1N1q0pr0=
+github.com/mitchellh/go-testing-interface v1.0.0/go.mod h1:kRemZodwjscx+RGhAo8eIhFbs2+BFgRtFPeD/KE+zxI=
+github.com/mitchellh/gox v0.4.0/go.mod h1:Sd9lOJ0+aimLBi73mGofS1ycjY8lL3uZM3JPS42BGNg=
+github.com/mitchellh/iochan v1.0.0/go.mod h1:JwYml1nuB7xOzsp52dPpHFffvOCDupsG0QubkSMEySY=
+github.com/mitchellh/mapstructure v0.0.0-20160808181253-ca63d7c062ee/go.mod h1:FVVH3fgwuzCH5S8UJGiWEs2h04kUh9fWfEaFds41c1Y=
+github.com/mitchellh/mapstructure v1.1.2/go.mod h1:FVVH3fgwuzCH5S8UJGiWEs2h04kUh9fWfEaFds41c1Y=
+github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd/go.mod h1:6dJC0mAP4ikYIbvyc7fijjWJddQyLn8Ig3JB5CqoB9Q=
+github.com/modern-go/reflect2 v1.0.1/go.mod h1:bx2lNnkwVCuqBIxFjflWJWanXIb3RllmbCylyMrvgv0=
+github.com/mwitkow/go-conntrack v0.0.0-20161129095857-cc309e4a2223/go.mod h1:qRWi+5nqEBWmkhHvq77mSJWrCKwh8bxhgT7d/eI7P4U=
+github.com/oklog/ulid v1.3.1/go.mod h1:CirwcVhetQ6Lv90oh/F+FBtV6XMibvdAFo93nm5qn4U=
+github.com/pascaldekloe/goe v0.0.0-20180627143212-57f6aae5913c/go.mod h1:lzWF7FIEvWOWxwDKqyGYQf6ZUaNfKdP144TG7ZOy1lc=
+github.com/pelletier/go-toml v1.2.0/go.mod h1:5z9KED0ma1S8pY6P1sdut58dfprrGBbd/94hg7ilaic=
+github.com/pkg/errors v0.8.0/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
+github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
+github.com/pkg/errors v0.9.1 h1:FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4=
+github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
+github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
+github.com/posener/complete v1.1.1/go.mod h1:em0nMJCgc9GFtwrmVmEMR/ZL6WyhyjMBndrE9hABlRI=
+github.com/prometheus/client_golang v0.9.1/go.mod h1:7SWBe2y4D6OKWSNQJUaRYU/AaXPKyh/dDVn+NZz0KFw=
+github.com/prometheus/client_golang v0.9.3/go.mod h1:/TN21ttK/J9q6uSwhBd54HahCDft0ttaMvbicHlPoso=
+github.com/prometheus/client_model v0.0.0-20180712105110-5c3871d89910/go.mod h1:MbSGuTsp3dbXC40dX6PRTWyKYBIrTGTE9sqQNg2J8bo=
+github.com/prometheus/client_model v0.0.0-20190129233127-fd36f4220a90/go.mod h1:xMI15A0UPsDsEKsMN9yxemIoYk6Tm2C1GtYGdfGttqA=
+github.com/prometheus/common v0.0.0-20181113130724-41aa239b4cce/go.mod h1:daVV7qP5qjZbuso7PdcryaAu0sAZbrN9i7WWcTMWvro=
+github.com/prometheus/common v0.4.0/go.mod h1:TNfzLD0ON7rHzMJeJkieUDPYmFC7Snx/y86RQel1bk4=
+github.com/prometheus/procfs v0.0.0-20181005140218-185b4288413d/go.mod h1:c3At6R/oaqEKCNdg8wHV1ftS6bRYblBhIjjI8uT2IGk=
+github.com/prometheus/procfs v0.0.0-20190507164030-5867b95ac084/go.mod h1:TjEm7ze935MbeOT/UhFTIMYKhuLP4wbCsTZCD3I8kEA=
+github.com/prometheus/tsdb v0.7.1/go.mod h1:qhTCs0VvXwvX/y3TZrWD7rabWM+ijKTux40TwIPHuXU=
+github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 h1:OdAsTTz6OkFY5QxjkYwrChwuRruF69c169dPK26NUlk=
+github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0/go.mod h1:qqbHyh8v60DhA7CoWK5oRCqLrMHRGoxYCSS9EjAz6Eo=
+github.com/rogpeppe/fastuuid v0.0.0-20150106093220-6724a57986af/go.mod h1:XWv6SoW27p1b0cqNHllgS5HIMJraePCO15w5zCzIWYg=
+github.com/rogpeppe/go-internal v1.3.0/go.mod h1:M8bDsm7K2OlrFYOpmOWEs/qY81heoFRclV5y23lUDJ4=
+github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
+github.com/ryanuber/columnize v0.0.0-20160712163229-9b3edd62028f/go.mod h1:sm1tb6uqfes/u+d4ooFouqFdy9/2g9QGwK3SQygK0Ts=
+github.com/sean-/seed v0.0.0-20170313163322-e2103e2c3529/go.mod h1:DxrIzT+xaE7yg65j358z/aeFdxmN0P9QXhEzd20vsDc=
+github.com/shenwei356/bio v0.0.0-20201213090627-18e3e643a476 h1:PE3sUBFeHWFNLsrQ7Blyk4duI+emVGKQ1+iYo4ZalKk=
+github.com/shenwei356/bio v0.0.0-20201213090627-18e3e643a476/go.mod h1:tKIebGVfqYwgLIoXohkLiQO685B2d3l9vTf1cjRZaVk=
+github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403 h1:/3JklLnHXiWUBxWc3joQYavDQJpncRhRA909cUb7eOw=
+github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403/go.mod h1:YkgdTWfNnJgv5HVJbVSDmxQtkK3/jZWDoqcG26BVU8k=
+github.com/shenwei356/breader v0.0.0-20170924140440-21f0a70fe179 h1:MZiEG6aN8j1A0jXzCzyZM2BM6ZHbePYiwR4FXgUTCCk=
+github.com/shenwei356/breader v0.0.0-20170924140440-21f0a70fe179/go.mod h1:Yb9qYJ2qJolWeqIVS1LG5ylHTLI5ZfbVFEJJouF2DsY=
+github.com/shenwei356/bwt v0.0.0-20200418151221-ae79c9858c90 h1:c8Er9GmVclwt002/ZxVx7WOThpmPKNR4rehAXxICTII=
+github.com/shenwei356/bwt v0.0.0-20200418151221-ae79c9858c90/go.mod h1:q4esDgocpgU8CcnXuPNun+hGv+VDXGX+NnXHQaHGRCU=
+github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba h1:UvnrxFDPmz7agYX0eQ2JEorTKn1ORnZ9dT5OzbjPvK8=
+github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba/go.mod h1:LiqYp/K5yCEWOi7Ux/iOF/kjDxtsdYjOGcKHDbEOXFU=
+github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d h1:eeXLHcXyGEr72V1SOSEI7vSzUOTJvHutwF7Ykm+hscQ=
+github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d/go.mod h1:SiiGiRFyRtV7S9RamOrmQR5gpGIRhWJM1w0EtmuQ1io=
+github.com/shenwei356/util v0.0.0-20201214054755-2942125340cd h1:11sa/TyR/91v63OA9VnyjRontqtsDFZN1wCLNaaAa38=
+github.com/shenwei356/util v0.0.0-20201214054755-2942125340cd/go.mod h1:n3qhc3bQzlqJ2/5v79hgl0Gd3WzJOkI8XcUix25Brdg=
+github.com/shenwei356/xopen v0.0.0-20181203091311-f4f16ddd3992 h1:RXEEyKj0JL3SrRIYsWIEyy4AwjHbI3I8aDGK6CA4+YI=
+github.com/shenwei356/xopen v0.0.0-20181203091311-f4f16ddd3992/go.mod h1:6EQUa6I7Zsl2GQKqcL9qGLrTzVE+oZyly+uhzovQYSk=
+github.com/shurcooL/sanitized_anchor_name v1.0.0/go.mod h1:1NzhyTcUVG4SuEtjjoZeVRXNmyL/1OwPU0+IJeTBvfc=
+github.com/sirupsen/logrus v1.2.0/go.mod h1:LxeOpSwHxABJmUn/MG1IvRgCAasNZTLOkJPxbbu5VWo=
+github.com/smallfish/simpleyaml v0.0.0-20170911015856-a32031077861 h1:9z0Ip656Pc+3cj/BpHkErOVg4iE0xcAdvJwfA3hMVzU=
+github.com/smallfish/simpleyaml v0.0.0-20170911015856-a32031077861/go.mod h1:eGZ1jp5PTJ+XVhTErUmw0xyPbgctPFlixWPypUrDkSs=
+github.com/smartystreets/assertions v0.0.0-20180927180507-b2de0cb4f26d/go.mod h1:OnSkiWE9lh6wB0YB77sQom3nweQdgAjqCqsofrRNTgc=
+github.com/smartystreets/goconvey v1.6.4/go.mod h1:syvi0/a8iFYH4r/RixwvyeAJjdLS9QV7WQ/tjFTllLA=
+github.com/soheilhy/cmux v0.1.4/go.mod h1:IM3LyeVVIOuxMH7sFAkER9+bJ4dT7Ms6E4xg4kGIyLM=
+github.com/spaolacci/murmur3 v0.0.0-20180118202830-f09979ecbc72 h1:qLC7fQah7D6K1B0ujays3HV9gkFtllcxhzImRR7ArPQ=
+github.com/spaolacci/murmur3 v0.0.0-20180118202830-f09979ecbc72/go.mod h1:JwIasOWyU6f++ZhiEuf87xNszmSA2myDM2Kzu9HwQUA=
+github.com/spf13/afero v1.1.2/go.mod h1:j4pytiNVoe2o6bmDsKpLACNPDBIoEAkihy7loJ1B0CQ=
+github.com/spf13/cast v1.3.0/go.mod h1:Qx5cxh0v+4UWYiBimWS+eyWzqEqokIECu5etghLkUJE=
+github.com/spf13/cobra v1.1.1 h1:KfztREH0tPxJJ+geloSLaAkaPkr4ki2Er5quFV1TDo4=
+github.com/spf13/cobra v1.1.1/go.mod h1:WnodtKOvamDL/PwE2M4iKs8aMDBZ5Q5klgD3qfVJQMI=
+github.com/spf13/jwalterweatherman v1.0.0/go.mod h1:cQK4TGJAtQXfYWX+Ddv3mKDzgVb68N+wFjFa4jdeBTo=
+github.com/spf13/pflag v1.0.3/go.mod h1:DYY7MBk1bdzusC3SYhjObp+wFpr4gzcvqqNjLnInEg4=
+github.com/spf13/pflag v1.0.5 h1:iy+VFUOCP1a+8yFto/drg2CJ5u0yRoB7fZw3DKv/JXA=
+github.com/spf13/pflag v1.0.5/go.mod h1:McXfInJRrz4CZXVZOBLb0bTZqETkiAhM9Iw0y3An2Bg=
+github.com/spf13/viper v1.7.0/go.mod h1:8WkrPz2fc9jxqZNCJI/76HCieCp4Q8HaLFoCha5qpdg=
+github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
+github.com/stretchr/objx v0.1.1/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
+github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs=
+github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI=
+github.com/subosito/gotenv v1.2.0/go.mod h1:N0PQaV/YGNqwC0u51sEeR/aUtSLEXKX9iv69rRypqCw=
+github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939 h1:BhIUXV2ySTLrKgh/Hnts+QTQlIbWtomXt3LMdzME0A0=
+github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939/go.mod h1:omGxs4/6hNjxPKUTjmaNkPzehSnNJOJN6pMEbrlYIT4=
+github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U=
+github.com/ulikunitz/xz v0.5.6/go.mod h1:2bypXElzHzzJZwzH67Y6wb67pO62Rzfn7BSiF4ABRW8=
+github.com/xiang90/probing v0.0.0-20190116061207-43a291ad63a2/go.mod h1:UETIi67q53MR2AWcXfiuqkDkRtnGDLqkBTpCHuJHxtU=
+go.etcd.io/bbolt v1.3.2/go.mod h1:IbVyRI1SCnLcuJnV2u8VeU0CEYM7e686BmAb1XKL+uU=
+go.opencensus.io v0.21.0/go.mod h1:mSImk1erAIZhrmZN+AvHh14ztQfjbGwt4TtuofqLduU=
+go.opencensus.io v0.22.0/go.mod h1:+kGneAE2xo2IficOXnaByMWTGM9T73dGwxeWcUqIpI8=
+go.uber.org/atomic v1.4.0/go.mod h1:gD2HeocX3+yG+ygLZcrzQJaqmWj9AIm7n08wl/qW/PE=
+go.uber.org/multierr v1.1.0/go.mod h1:wR5kodmAFQ0UK8QlbwjlSNy0Z68gJhDJUG5sjR94q/0=
+go.uber.org/zap v1.10.0/go.mod h1:vwi/ZaCAaUcBkycHslxD9B2zi4UTXhF60s6SWpuDF0Q=
+golang.org/x/crypto v0.0.0-20180904163835-0709b304e793/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4=
+golang.org/x/crypto v0.0.0-20181029021203-45a5f77698d3/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4=
+golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
+golang.org/x/crypto v0.0.0-20190510104115-cbcb75029529/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
+golang.org/x/crypto v0.0.0-20190605123033-f99c8df09eb5 h1:58fnuSXlxZmFdJyvtTFVmVhcMLU6v5fEb/ok4wyqtNU=
+golang.org/x/crypto v0.0.0-20190605123033-f99c8df09eb5/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
+golang.org/x/exp v0.0.0-20180321215751-8460e604b9de/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
+golang.org/x/exp v0.0.0-20180807140117-3d87b88a115f/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
+golang.org/x/exp v0.0.0-20190121172915-509febef88a4/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
+golang.org/x/exp v0.0.0-20190306152737-a1d7652674e8/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
+golang.org/x/exp v0.0.0-20190510132918-efd6b22b2522/go.mod h1:ZjyILWgesfNpC6sMxTJOJm9Kp84zZh5NQWvqDGG3Qr8=
+golang.org/x/exp v0.0.0-20190829153037-c13cbed26979/go.mod h1:86+5VVa7VpoJ4kLfm080zCjGlMRFzhUhsZKEZO7MGek=
+golang.org/x/exp v0.0.0-20191030013958-a1ab85dbe136/go.mod h1:JXzH8nQsPlswgeRAPE3MuO9GYsAcnJvJ4vnMwN/5qkY=
+golang.org/x/exp v0.0.0-20200119233911-0405dc783f0a h1:7Wlg8L54In96HTWOaI4sreLJ6qfyGuvSau5el3fK41Y=
+golang.org/x/exp v0.0.0-20200119233911-0405dc783f0a/go.mod h1:2RIsYlXP63K8oxa1u096TMicItID8zy7Y6sNkU49FU4=
+golang.org/x/image v0.0.0-20180708004352-c73c2afc3b81/go.mod h1:ux5Hcp/YLpHSI86hEcLt0YII63i6oz57MZXIpbrjZUs=
+golang.org/x/image v0.0.0-20190227222117-0694c2d4d067/go.mod h1:kZ7UVZpmo3dzQBMxlp+ypCbDeSB+sBbTgSJuh5dn5js=
+golang.org/x/image v0.0.0-20190802002840-cff245a6509b h1:+qEpEAPhDZ1o0x3tHzZTQDArnOixOzGD9HUJfcg0mb4=
+golang.org/x/image v0.0.0-20190802002840-cff245a6509b/go.mod h1:FeLwcggjj3mMvU+oOTbSwawSJRM1uh48EjtB4UJZlP0=
+golang.org/x/lint v0.0.0-20181026193005-c67002cb31c3/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE=
+golang.org/x/lint v0.0.0-20190227174305-5b3e6a55c961/go.mod h1:wehouNa3lNwaWXcvxsM5YxQ5yQlVC4a0KAMCusXpPoU=
+golang.org/x/lint v0.0.0-20190301231843-5614ed5bae6f/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE=
+golang.org/x/lint v0.0.0-20190313153728-d0100b6bd8b3/go.mod h1:6SW0HCj/g11FgYtHlgUYUwCkIfeOF89ocIRzGO/8vkc=
+golang.org/x/lint v0.0.0-20190409202823-959b441ac422/go.mod h1:6SW0HCj/g11FgYtHlgUYUwCkIfeOF89ocIRzGO/8vkc=
+golang.org/x/lint v0.0.0-20190909230951-414d861bb4ac/go.mod h1:6SW0HCj/g11FgYtHlgUYUwCkIfeOF89ocIRzGO/8vkc=
+golang.org/x/lint v0.0.0-20190930215403-16217165b5de/go.mod h1:6SW0HCj/g11FgYtHlgUYUwCkIfeOF89ocIRzGO/8vkc=
+golang.org/x/mobile v0.0.0-20190312151609-d3739f865fa6/go.mod h1:z+o9i4GpDbdi3rU15maQ/Ox0txvL9dWGYEHz965HBQE=
+golang.org/x/mobile v0.0.0-20190719004257-d2bd2a29d028/go.mod h1:E/iHnbuqvinMTCcRqshq8CkpyQDoeVncDDYHnLhea+o=
+golang.org/x/mod v0.0.0-20190513183733-4bf6d317e70e/go.mod h1:mXi4GBBbnImb6dmsKGUJ2LatrhH/nqhxcFungHvyanc=
+golang.org/x/mod v0.1.0/go.mod h1:0QHyrYULN0/3qlju5TqG8bIK38QM8yzMo5ekMj3DlcY=
+golang.org/x/net v0.0.0-20180724234803-3673e40ba225/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
+golang.org/x/net v0.0.0-20180826012351-8a410e7b638d/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
+golang.org/x/net v0.0.0-20181023162649-9b4f9f5ad519/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
+golang.org/x/net v0.0.0-20181114220301-adae6a3d119a/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
+golang.org/x/net v0.0.0-20181201002055-351d144fa1fc/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
+golang.org/x/net v0.0.0-20181220203305-927f97764cc3/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
+golang.org/x/net v0.0.0-20190108225652-1e06a53dbb7e/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
+golang.org/x/net v0.0.0-20190213061140-3a22650c66bd/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
+golang.org/x/net v0.0.0-20190311183353-d8887717615a/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
+golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
+golang.org/x/net v0.0.0-20190501004415-9ce7a6920f09/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
+golang.org/x/net v0.0.0-20190503192946-f4e77d36d62c/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
+golang.org/x/net v0.0.0-20190603091049-60506f45cf65/go.mod h1:HSz+uSET+XFnRR8LxR5pz3Of3rY3CfYBVs4xY44aLks=
+golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
+golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be/go.mod h1:N/0e6XlmueqKjAGxoOufVs8QHGRruUQn6yWY3a++T0U=
+golang.org/x/oauth2 v0.0.0-20190226205417-e64efc72b421/go.mod h1:gOpvHmFTYa4IltrdGE7lF6nIHvwfUNPOp7c8zoXwtLw=
+golang.org/x/oauth2 v0.0.0-20190604053449-0f29369cfe45/go.mod h1:gOpvHmFTYa4IltrdGE7lF6nIHvwfUNPOp7c8zoXwtLw=
+golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
+golang.org/x/sync v0.0.0-20181108010431-42b317875d0f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
+golang.org/x/sync v0.0.0-20181221193216-37e7f081c4d4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
+golang.org/x/sync v0.0.0-20190227155943-e225da77a7e6/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
+golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
+golang.org/x/sys v0.0.0-20180823144017-11551d06cbcc/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/sys v0.0.0-20180905080454-ebe1bf3edb33/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/sys v0.0.0-20181026203630-95b1ffbd15a5/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/sys v0.0.0-20181107165924-66b7b1311ac8/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/sys v0.0.0-20181116152217-5ac8a444bdc5/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
+golang.org/x/sys v0.0.0-20190312061237-fead79001313/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20190502145724-3ef323f4f1fd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20190507160741-ecd444e8653b/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20190602015325-4c4f7f33c9ed/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20190606165138-5da285871e9c/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20190624142023-c5567b49c5d0/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20191005200804-aed5e4c7ecf9/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20200116001909-b77594299b42/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae h1:/WDfKMnPU+m5M4xB+6x4kaepxRw6jWvR5iDRdvjHgy8=
+golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
+golang.org/x/text v0.3.1-0.20180807135948-17ff2d5776d2/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
+golang.org/x/text v0.3.2/go.mod h1:bEr9sfX3Q8Zfm5fL9x+3itogRgK3+ptLWKqgva+5dAk=
+golang.org/x/time v0.0.0-20181108054448-85acf8d2951c/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ=
+golang.org/x/time v0.0.0-20190308202827-9d24e82272b4/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ=
+golang.org/x/tools v0.0.0-20180221164845-07fd8470d635/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
+golang.org/x/tools v0.0.0-20180525024113-a5b4c53f6e8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
+golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
+golang.org/x/tools v0.0.0-20190114222345-bf090417da8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
+golang.org/x/tools v0.0.0-20190226205152-f727befe758c/go.mod h1:9Yl7xja0Znq3iFh3HoIrodX9oNMXvdceNzlUR8zjMvY=
+golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=
+golang.org/x/tools v0.0.0-20190312151545-0bb0c0a6e846/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=
+golang.org/x/tools v0.0.0-20190312170243-e65039ee4138/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=
+golang.org/x/tools v0.0.0-20190328211700-ab21143f2384/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=
+golang.org/x/tools v0.0.0-20190425150028-36563e24a262/go.mod h1:RgjU9mgBXZiqYHBnxXauZ1Gv1EHHAz9KjViQ78xBX0Q=
+golang.org/x/tools v0.0.0-20190506145303-2d16b83fe98c/go.mod h1:RgjU9mgBXZiqYHBnxXauZ1Gv1EHHAz9KjViQ78xBX0Q=
+golang.org/x/tools v0.0.0-20190606050223-4d9ae51c2468/go.mod h1:/rFqwRUd4F7ZHNgwSSTFct+R/Kf4OFW1sUzUTQQTgfc=
+golang.org/x/tools v0.0.0-20190606124116-d0a3d012864b/go.mod h1:/rFqwRUd4F7ZHNgwSSTFct+R/Kf4OFW1sUzUTQQTgfc=
+golang.org/x/tools v0.0.0-20190621195816-6e04913cbbac/go.mod h1:/rFqwRUd4F7ZHNgwSSTFct+R/Kf4OFW1sUzUTQQTgfc=
+golang.org/x/tools v0.0.0-20190628153133-6cdbf07be9d0/go.mod h1:/rFqwRUd4F7ZHNgwSSTFct+R/Kf4OFW1sUzUTQQTgfc=
+golang.org/x/tools v0.0.0-20190816200558-6889da9d5479/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
+golang.org/x/tools v0.0.0-20190911174233-4f2ddba30aff/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
+golang.org/x/tools v0.0.0-20191012152004-8de300cfc20a/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
+golang.org/x/tools v0.0.0-20191112195655-aa38f8e97acc/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
+golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
+gonum.org/v1/gonum v0.0.0-20180816165407-929014505bf4 h1:nYxTaCPaVoJbxx+vMVnsFb6kw5+6aJCx52m/lmM/Vog=
+gonum.org/v1/gonum v0.0.0-20180816165407-929014505bf4/go.mod h1:Y+Yx5eoAFn32cQvJDxZx5Dpnq+c3wtXuadVZAcxbbBo=
+gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b h1:Qh4dB5D/WpoUUp3lSod7qgoyEHbDGPUWjIbnqdqqe1k=
+gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b/go.mod h1:Wt8AAjI+ypCyYX3nZBvf6cAIx93T+c/OS2HFAYskSZc=
+google.golang.org/api v0.4.0/go.mod h1:8k5glujaEP+g9n7WNsDg8QP6cUVNI86fCNMcbazEtwE=
+google.golang.org/api v0.7.0/go.mod h1:WtwebWUNSVBH/HAw79HIFXZNqEvBhG+Ra+ax0hx3E3M=
+google.golang.org/api v0.8.0/go.mod h1:o4eAsZoiT+ibD93RtjEohWalFOjRDx6CVaqeizhEnKg=
+google.golang.org/api v0.9.0/go.mod h1:o4eAsZoiT+ibD93RtjEohWalFOjRDx6CVaqeizhEnKg=
+google.golang.org/api v0.13.0/go.mod h1:iLdEw5Ide6rF15KTC1Kkl0iskquN2gFfn9o9XIsbkAI=
+google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM=
+google.golang.org/appengine v1.4.0/go.mod h1:xpcJRLb0r/rnEns0DIKYYv+WjYCduHsrkT7/EB5XEv4=
+google.golang.org/appengine v1.5.0/go.mod h1:xpcJRLb0r/rnEns0DIKYYv+WjYCduHsrkT7/EB5XEv4=
+google.golang.org/appengine v1.6.1/go.mod h1:i06prIuMbXzDqacNJfV5OdTW448YApPu5ww/cMBSeb0=
+google.golang.org/genproto v0.0.0-20180817151627-c66870c02cf8/go.mod h1:JiN7NxoALGmiZfu7CAH4rXhgtRTLTxftemlI0sWmxmc=
+google.golang.org/genproto v0.0.0-20190307195333-5fe7a883aa19/go.mod h1:VzzqZJRnGkLBvHegQrXjBqPurQTc5/KpmUdxsrq26oE=
+google.golang.org/genproto v0.0.0-20190418145605-e7d98fc518a7/go.mod h1:VzzqZJRnGkLBvHegQrXjBqPurQTc5/KpmUdxsrq26oE=
+google.golang.org/genproto v0.0.0-20190425155659-357c62f0e4bb/go.mod h1:VzzqZJRnGkLBvHegQrXjBqPurQTc5/KpmUdxsrq26oE=
+google.golang.org/genproto v0.0.0-20190502173448-54afdca5d873/go.mod h1:VzzqZJRnGkLBvHegQrXjBqPurQTc5/KpmUdxsrq26oE=
+google.golang.org/genproto v0.0.0-20190801165951-fa694d86fc64/go.mod h1:DMBHOl98Agz4BDEuKkezgsaosCRResVns1a3J2ZsMNc=
+google.golang.org/genproto v0.0.0-20190819201941-24fa4b261c55/go.mod h1:DMBHOl98Agz4BDEuKkezgsaosCRResVns1a3J2ZsMNc=
+google.golang.org/genproto v0.0.0-20190911173649-1774047e7e51/go.mod h1:IbNlFCBrqXvoKpeg0TB2l7cyZUmoaFKYIwrEpbDKLA8=
+google.golang.org/genproto v0.0.0-20191108220845-16a3f7862a1a/go.mod h1:n3cpQtvxv34hfy77yVDNjmbRyujviMdxYliBSkLhpCc=
+google.golang.org/grpc v1.19.0/go.mod h1:mqu4LbDTu4XGKhr4mRzUsmM4RtVoemTSY81AxZiDr8c=
+google.golang.org/grpc v1.20.1/go.mod h1:10oTOabMzJvdu6/UiuZezV6QK5dSlG84ov/aaiqXj38=
+google.golang.org/grpc v1.21.1/go.mod h1:oYelfM1adQP15Ek0mdvEgi9Df8B9CZIaU1084ijfRaM=
+gopkg.in/alecthomas/kingpin.v2 v2.2.6/go.mod h1:FMv+mEhP44yOT+4EoQTLFTRgOQ1FBLkstjWtayDeSgw=
+gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
+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
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20210114/ecdc8b96/attachment-0001.html>
More information about the debian-med-commit
mailing list