amplicon: fix BED coordinates for amplicons found in the minus strand. …

…#367
shenwei356 · Feb 20, 2023 · 1bb0cc6 · 1bb0cc6
1 parent 15b1662
commit 1bb0cc6
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Showing 5 changed files with 207 additions and 37 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,8 @@
         - do not append space if there's no description after the sequene ID.
     - `seqkit sliding`:
         - new flag `-S/--suffix` for change the suffix added to the sequence ID (default: _sliding).
+    - `seqkit amplicon`:
+        - fix BED coordinates for amplicons found in the minus strand. [#367](https://github.com/shenwei356/seqkit/issues/367)
 - [SeqKit v2.3.1](https://github.com/shenwei356/seqkit/releases/tag/v2.3.1) - 2022-09-22
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/seqkit/v2.3.1/total.svg)](https://github.com/shenwei356/seqkit/releases/tag/v2.3.1)
     - `seqkit grep/locate`: fix bug of FMIndex building for empty sequences. [#321](https://github.com/shenwei356/seqkit/issues/321)

diff --git a/doc/docs/usage.md b/doc/docs/usage.md
@@ -2114,7 +2114,7 @@ Examples
         seq1    3       13      p1      0       +       CCCACTGAAA
         seq1    1       7       p4      0       +       CGCCCA
         seq1    3       13      p2      0       -       TTTCAGTGGG
-        seq1    3       6       p3      0       -       TTT
+        seq1    10      13      p3      0       -       TTT
         seq2    1       17      p4      0       +       CGTACGGTCAGATCCA
         seq2    1       15      P5      0       +       CGTACGGTCAGATC
         seq2    3       17      p6      0       +       TACGGTCAGATCCA

diff --git a/go.mod b/go.mod
@@ -5,6 +5,7 @@ go 1.17
 require (
 	github.com/biogo/biogo v1.0.4
 	github.com/biogo/hts v1.4.4
+	github.com/botond-sipos/thist v1.1.0
 	github.com/cespare/xxhash/v2 v2.1.2
 	github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8
 	github.com/dustin/go-humanize v1.0.0
@@ -33,15 +34,26 @@ require (
 replace github.com/miekg/dns v1.0.14 => github.com/miekg/dns v1.1.46
 
 require (
+	git.sr.ht/~sbinet/gg v0.3.1 // indirect
+	github.com/ajstarks/svgo v0.0.0-20211024235047-1546f124cd8b // indirect
 	github.com/davecgh/go-spew v1.1.1 // indirect
 	github.com/edsrzf/mmap-go v1.1.0 // indirect
+	github.com/go-fonts/liberation v0.2.0 // indirect
+	github.com/go-latex/latex v0.0.0-20210823091927-c0d11ff05a81 // indirect
+	github.com/go-pdf/fpdf v0.6.0 // indirect
+	github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0 // indirect
 	github.com/inconshreveable/mousetrap v1.0.1 // indirect
 	github.com/mattn/go-runewidth v0.0.14 // indirect
 	github.com/rivo/uniseg v0.4.2 // indirect
 	github.com/rogpeppe/go-internal v1.9.0 // indirect
 	github.com/shenwei356/natsort v0.0.0-20220117010048-580176ad49fb // indirect
 	github.com/spf13/pflag v1.0.5 // indirect
+	golang.org/x/crypto v0.0.0-20220919173607-35f4265a4bc0 // indirect
+	golang.org/x/image v0.0.0-20220902085622-e7cb96979f69 // indirect
 	golang.org/x/sys v0.0.0-20220919091848-fb04ddd9f9c8 // indirect
+	golang.org/x/term v0.0.0-20220919170432-7a66f970e087 // indirect
+	golang.org/x/text v0.3.7 // indirect
+	gonum.org/v1/plot v0.12.0 // indirect
 	gopkg.in/yaml.v2 v2.4.0 // indirect
 	gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b // indirect
 )