Merge pull request #18 from release/0.5.1

Update to 0.5.1

CHANGELOG.md

@@ -1,5 +1,8 @@
 # Changelog
 
+## 0.5.1
+- Fix exon sorting to take the transcirpt orientation into account
+
 ## 0.5
 - Add exon numbers in GTF output
 - Refactor GTF parsing to improve performance

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "atg"
-version = "0.5.0"
+version = "0.5.1"
 authors = ["Jonas Marcello <[email protected]>"]
 edition = "2018"
 description = "A utility to handle transcripts for genomics and transcriptomics"
@@ -12,6 +12,7 @@ keywords = ["bioinformatics", "genomics", "transcriptomics", "transcript", "gene
 categories = ["science", "data-structures", "command-line-utilities"]
 
 [dependencies]
+atglib = "0.1"
 clap = "2.33.3"
 log = "0.4"
 loggerv = "0.7"

JUSTFILE

@@ -58,7 +58,11 @@ test:
     echo -ne "Checking exon numbering in exon, CDS, and UTR"
     (diff <( cargo run -- -f refgene -i tests/data/example.refgene -t gtf -g ncbiRefSeq.2021-05-17 -o /dev/stdout 2> /dev/null | grep "\texon\t" | grep "NM_004015.3.18" | wc -l | sed "s/ //g") <(echo "1") && \
     diff <( cargo run -- -f refgene -i tests/data/example.refgene -t gtf -g ncbiRefSeq.2021-05-17 -o /dev/stdout 2> /dev/null | grep "\tCDS\t" | grep "NM_004015.3.18" | wc -l | sed "s/ //g") <(echo "1") && \
-    diff <( cargo run -- -f refgene -i tests/data/example.refgene -t gtf -g ncbiRefSeq.2021-05-17 -o /dev/stdout 2> /dev/null | grep "\t5UTR\t" | grep "NM_004015.3.18" | wc -l | sed "s/ //g") <(echo "1") && \
+    diff <( cargo run -- -f refgene -i tests/data/example.refgene -t gtf -g ncbiRefSeq.2021-05-17 -o /dev/stdout 2> /dev/null | grep "\t5UTR\t" | grep "NM_004015.3.18" | wc -l | sed "s/ //g") <(echo "0") && \
+    diff <( cargo run -- -f refgene -i tests/data/example.refgene -t gtf -g ncbiRefSeq.2021-05-17 -o /dev/stdout 2> /dev/null | grep "\t5UTR\t" | grep "NM_004015.3.0" | wc -l | sed "s/ //g") <(echo "0") && \
+    diff <( cargo run -- -f refgene -i tests/data/example.refgene -t gtf -g ncbiRefSeq.2021-05-17 -o /dev/stdout 2> /dev/null | grep "\t5UTR\t" | grep "NM_004015.3.1" | wc -l | sed "s/ //g") <(echo "1") && \
+    diff <( cargo run -- -f refgene -i tests/data/example.refgene -t gtf -g ncbiRefSeq.2021-05-17 -o /dev/stdout 2> /dev/null | grep "\t5UTR\t" | grep "NM_004015.3.2" | wc -l | sed "s/ //g") <(echo "0") && \
+    diff <( cargo run -- -f refgene -i tests/data/example.refgene -t gtf -g ncbiRefSeq.2021-05-17 -o /dev/stdout 2> /dev/null | grep "\t3UTR\t" | grep "NM_004015.3.18" | wc -l | sed "s/ //g") <(echo "1") && \
     diff <( cargo run -- -f refgene -i tests/data/example.refgene -t gtf -g ncbiRefSeq.2021-05-17 -o /dev/stdout 2> /dev/null | grep "NM_004015.3.18" | wc -l | sed "s/ //g") <(echo "3") && \
     echo " \e[32m\e[1mOK\e[0m") || echo "\e[31m\e[1mERROR\e[0m"