From e322533f2f8a50187273bb2a02177b9bb48c6c2d Mon Sep 17 00:00:00 2001 From: Haibao Tang Date: Thu, 19 Dec 2024 18:19:35 -0800 Subject: [PATCH 1/4] update go version --- .github/workflows/build.yml | 2 +- tests/test.counts_RE.txt | 3 --- 2 files changed, 1 insertion(+), 4 deletions(-) delete mode 100644 tests/test.counts_RE.txt diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 1cb55fe..f2678a4 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -7,7 +7,7 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest] - go: [1.12, 1.16] + go: [1.16, 1.23] steps: - name: Set up Go ${{ matrix.go }} diff --git a/tests/test.counts_RE.txt b/tests/test.counts_RE.txt deleted file mode 100644 index 6cc6e46..0000000 --- a/tests/test.counts_RE.txt +++ /dev/null @@ -1,3 +0,0 @@ -#Contig RECounts Length -S_1 504 135917 -S_2689 532 149466 From d5bda71b76d058eadafcefe0e05e8baf5d2168e2 Mon Sep 17 00:00:00 2001 From: Haibao Tang Date: Thu, 19 Dec 2024 18:24:17 -0800 Subject: [PATCH 2/4] update with go mod tidy --- go.mod | 1 - go.sum | 27 ++------------------------- 2 files changed, 2 insertions(+), 26 deletions(-) diff --git a/go.mod b/go.mod index 4744d96..5edb377 100644 --- a/go.mod +++ b/go.mod @@ -27,6 +27,5 @@ require ( github.com/shenwei356/util v0.0.0-20201214054755-2942125340cd // indirect github.com/shenwei356/xopen v0.0.0-20181203091311-f4f16ddd3992 github.com/spf13/cobra v1.1.1 - github.com/ugorji/go v1.1.4 // indirect golang.org/x/sync v0.0.0-20201207232520-09787c993a3a // indirect ) diff --git a/go.sum b/go.sum index b2f0931..7ca3d5f 100644 --- a/go.sum +++ b/go.sum @@ -13,8 +13,6 @@ cloud.google.com/go/storage v1.0.0/go.mod h1:IhtSnM/ZTZV8YYJWCY8RULGVqBDmpoyjwiy 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/MaxHalford/eaopt v0.1.1-0.20200203085436-ba4b9950c779 h1:7F7eE8anpA9zlESucX52vK9PKJxTO+Nh9CFr6KIIyMQ= -github.com/MaxHalford/eaopt v0.1.1-0.20200203085436-ba4b9950c779/go.mod h1:/BtsvPTut6WckNrjS1D7MQRv9IOXnPN0lnrWIqyCFQI= github.com/MaxHalford/eaopt v0.4.2 h1:4o8MADAtpnkh7ENaEvaTjBQK35ArAmKCh8KFZvXtbSc= github.com/MaxHalford/eaopt v0.4.2/go.mod h1:cTz/IQazmJMSEllWjTzuReRUmLBR20o0C8OUoUHHuP8= github.com/OneOfOne/xxhash v1.2.2/go.mod h1:HSdplMjZKSmBqAxg5vPj2TmRDmfkzw+cTzAElWljhcU= @@ -29,8 +27,6 @@ github.com/beorn7/perks v1.0.0/go.mod h1:KWe93zE9D1o94FZ5RNwFwVgaQK1VOXiVxmqh+Ce github.com/bgentry/speakeasy v0.1.0/go.mod h1:+zsyZBPWlz7T6j88CTgSN5bM796AkVf0kBD4zp0CCIs= 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/hts v1.1.0 h1:J6Na8+e+MYyEpV1B762GUvt4mhtPn3tnQQaxWyKo5rk= -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/bketelsen/crypt v0.0.3-0.20200106085610-5cbc8cc4026c/go.mod h1:MKsuJmJgSg28kpZDP6UIiPt0e0Oz0kqKNGyRaWEPv84= @@ -64,12 +60,10 @@ github.com/go-kit/kit v0.8.0/go.mod h1:xBxKIO96dXMWWy0MnWVtmwkA9/13aqxPnvrjFYMA2 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/gobuffalo/envy v1.7.0 h1:GlXgaiBkmrYMHco6t4j7SacKO4XUjvh5pwXh0f4uxXU= github.com/gobuffalo/envy v1.7.0/go.mod h1:n7DRkBerg/aorDM8kbduw5dN3oXGswK5liaSCx4T5NI= github.com/gobuffalo/envy v1.9.0 h1:eZR0DuEgVLfeIb1zIKt3bT4YovIMf9O9LXQeCZLXpqE= github.com/gobuffalo/envy v1.9.0/go.mod h1:FurDp9+EDPE4aIUS3ZLyD+7/9fpx7YRt/ukY6jIHf0w= github.com/gobuffalo/logger v1.0.0/go.mod h1:2zbswyIUa45I+c+FLXuWl9zSWEiVuthsk8ze5s8JvPs= -github.com/gobuffalo/packd v0.3.0 h1:eMwymTkA1uXsqxS0Tpoop3Lc0u3kTfiMBE6nKtQU4g4= github.com/gobuffalo/packd v0.3.0/go.mod h1:zC7QkmNkYVGKPw4tHpBQ+ml7W/3tIebgeo1b36chA3Q= github.com/gobuffalo/packd v1.0.0 h1:6ERZvJHfe24rfFmA9OaoKBdC7+c9sydrytMg8SdFGBM= github.com/gobuffalo/packd v1.0.0/go.mod h1:6VTc4htmJRFB7u1m/4LeMTWjFoYrUiBkU9Fdec9hrhI= @@ -107,7 +101,6 @@ github.com/google/renameio v0.1.0/go.mod h1:KWCgfxg9yswjAJkECMjeO8J8rahYeXnNhOm4 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 v1.4.0/go.mod h1:E7qHFY5m1UJ88s3WnNqhKjPHQ0heANvMoAMk2YaljkQ= 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= @@ -144,12 +137,8 @@ github.com/julienschmidt/httprouter v1.2.0/go.mod h1:SYymIcj16QtmaHHD7aYtjjsJG7V github.com/karrick/godirwalk v1.10.12/go.mod h1:RoGL9dQei4vP9ilrpETWE8CLOZ1kiN0LhBygSwrAsHA= 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 v1.10.1 h1:a/QY0o9S6wCi0XhxaMX/QmusicNUqCqFugR6WKPOSoQ= -github.com/klauspost/compress v1.10.1/go.mod h1:aoV0uJVorq1K+umq18yTdKaF57EivdYsUV+/s2qKfXs= 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 v1.2.1 h1:oIPZROsWuPHpOdMVWLuJZXwgjhrW8r1yEX8UqMyeNHM= -github.com/klauspost/pgzip v1.2.1/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs= 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= @@ -206,7 +195,6 @@ github.com/remyoudompheng/bigfft v0.0.0-20190728182440-6a916e37a237 h1:HQagqIiBm github.com/remyoudompheng/bigfft v0.0.0-20190728182440-6a916e37a237/go.mod h1:qqbHyh8v60DhA7CoWK5oRCqLrMHRGoxYCSS9EjAz6Eo= github.com/rogpeppe/fastuuid v0.0.0-20150106093220-6724a57986af/go.mod h1:XWv6SoW27p1b0cqNHllgS5HIMJraePCO15w5zCzIWYg= github.com/rogpeppe/go-internal v1.1.0/go.mod h1:M8bDsm7K2OlrFYOpmOWEs/qY81heoFRclV5y23lUDJ4= -github.com/rogpeppe/go-internal v1.3.0 h1:RR9dF3JtopPvtkroDZuVD7qquD0bnHlKSqaQhgwt8yk= github.com/rogpeppe/go-internal v1.3.0/go.mod h1:M8bDsm7K2OlrFYOpmOWEs/qY81heoFRclV5y23lUDJ4= github.com/rogpeppe/go-internal v1.3.2/go.mod h1:xXDCJY+GAPziupqXw64V24skbSoqbTEfhy4qGm1nDQc= github.com/rogpeppe/go-internal v1.6.2 h1:aIihoIOHCiLZHxyoNQ+ABL4NKhFTgKLBdMLyEAh98m0= @@ -215,14 +203,10 @@ github.com/russross/blackfriday v1.5.2/go.mod h1:JO/DiYxRf+HjHt06OyowR9PTA263kcR 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 v0.0.0-20200221152329-23abb30d7f0f h1:3hokgk3w1FKx4h9xdPjGkOHJh+9YGC6TvMT0dqYB0y4= -github.com/shenwei356/bio v0.0.0-20200221152329-23abb30d7f0f/go.mod h1:tKIebGVfqYwgLIoXohkLiQO685B2d3l9vTf1cjRZaVk= 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/util v0.0.0-20190523143900-f71ff373860c h1:QzUSl2qAx7JrPwSDvL3A4AOfF3mebJMsBIjhQBCkUqo= -github.com/shenwei356/util v0.0.0-20190523143900-f71ff373860c/go.mod h1:n3qhc3bQzlqJ2/5v79hgl0Gd3WzJOkI8XcUix25Brdg= 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= @@ -237,27 +221,22 @@ github.com/spaolacci/murmur3 v0.0.0-20180118202830-f09979ecbc72/go.mod h1:JwIasO 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 v0.0.5/go.mod h1:3K3wKZymM7VvHMDS9+Akkh4K60UwM26emMESw8tLCHU= -github.com/spf13/cobra v0.0.6 h1:breEStsVwemnKh2/s6gMvSdMEkwW0sK8vGStnlVBMCs= -github.com/spf13/cobra v0.0.6/go.mod h1:/6GTrnGXV9HjY+aR4k0oJ5tcvakLuG6EuKReYlHNrgE= 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 h1:zPAT6CGy6wXeQ7NtTnaTerfKOsV6V6F8agHXFiazDkg= 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 v1.3.2/go.mod h1:ZiWeW+zYFKm7srdB9IoDzzZXaJaI5eL9QjNiN/DMA2s= -github.com/spf13/viper v1.4.0/go.mod h1:PTJ7Z/lr49W6bUbkmS1V3by4uWynFiR9p7+dSq/yZzE= 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 h1:TivCn/peBQ7UY8ooIcPgZFpTNSz0Q2U6UrFlUfqbe0Q= github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI= +github.com/stretchr/testify v1.4.0 h1:2E4SXV/wtOkTonXsotYi4li6zVWxYlZuYNCXe9XRJyk= github.com/stretchr/testify v1.4.0/go.mod h1:j7eGeouHqKxXV5pUuKE4zz7dFj8WfuZ+81PSLYec5m4= github.com/subosito/gotenv v1.2.0/go.mod h1:N0PQaV/YGNqwC0u51sEeR/aUtSLEXKX9iv69rRypqCw= github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U= -github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc= github.com/ugorji/go/codec v0.0.0-20181204163529-d75b2dcb6bc8/go.mod h1:VFNgLljTbGfSG7qAOspJ7OScBnGdDN/yBr0sguwnwf0= github.com/ulikunitz/xz v0.5.6/go.mod h1:2bypXElzHzzJZwzH67Y6wb67pO62Rzfn7BSiF4ABRW8= github.com/xiang90/probing v0.0.0-20190116061207-43a291ad63a2/go.mod h1:UETIi67q53MR2AWcXfiuqkDkRtnGDLqkBTpCHuJHxtU= @@ -306,7 +285,6 @@ golang.org/x/net v0.0.0-20190311183353-d8887717615a/go.mod h1:t9HGtf8HONx5eT2rtn 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 v0.0.0-20190522155817-f3200d17e092/go.mod h1:HSz+uSET+XFnRR8LxR5pz3Of3rY3CfYBVs4xY44aLks= 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= @@ -316,7 +294,6 @@ golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJ 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 h1:8gQV6CLnAEikrhgkHFbMAEhagSSnXWGV915qUMm9mrU= golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20201207232520-09787c993a3a h1:DcqTD9SDLc+1P/r1EmRBwnVsrOwW+kk2vWf9n+1sGhs= @@ -381,7 +358,6 @@ google.golang.org/genproto v0.0.0-20190911173649-1774047e7e51/go.mod h1:IbNlFCBr 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 v1.21.0/go.mod h1:oYelfM1adQP15Ek0mdvEgi9Df8B9CZIaU1084ijfRaM= 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= @@ -395,6 +371,7 @@ gopkg.in/yaml.v2 v2.0.0-20170812160011-eb3733d160e7/go.mod h1:JAlM8MvJe8wmxCU4Bl gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.2.2/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= From 4e39a11fd6b83ba41fb4f764d52dd5a007258008 Mon Sep 17 00:00:00 2001 From: Haibao Tang Date: Thu, 19 Dec 2024 18:28:34 -0800 Subject: [PATCH 3/4] Add the test file back --- tests/test.counts_RE.txt | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 tests/test.counts_RE.txt diff --git a/tests/test.counts_RE.txt b/tests/test.counts_RE.txt new file mode 100644 index 0000000..6cc6e46 --- /dev/null +++ b/tests/test.counts_RE.txt @@ -0,0 +1,3 @@ +#Contig RECounts Length +S_1 504 135917 +S_2689 532 149466 From 6723bbdf33d4a9f5cf7fc76ece474995c8199301 Mon Sep 17 00:00:00 2001 From: Haibao Tang Date: Thu, 19 Dec 2024 18:29:37 -0800 Subject: [PATCH 4/4] remove ossar --- .github/workflows/ossar-analysis.yml | 49 ---------------------------- 1 file changed, 49 deletions(-) delete mode 100644 .github/workflows/ossar-analysis.yml diff --git a/.github/workflows/ossar-analysis.yml b/.github/workflows/ossar-analysis.yml deleted file mode 100644 index 86a27ac..0000000 --- a/.github/workflows/ossar-analysis.yml +++ /dev/null @@ -1,49 +0,0 @@ -# This workflow integrates a collection of open source static analysis tools -# with GitHub code scanning. For documentation, or to provide feedback, visit -# https://github.com/github/ossar-action -name: OSSAR - -on: - push: - pull_request: - -jobs: - OSSAR-Scan: - # OSSAR runs on windows-latest. - # ubuntu-latest and macos-latest support coming soon - runs-on: windows-latest - - steps: - # Checkout your code repository to scan - - name: Checkout repository - uses: actions/checkout@v2 - with: - # We must fetch at least the immediate parents so that if this is - # a pull request then we can checkout the head. - fetch-depth: 2 - - # If this run was triggered by a pull request event, then checkout - # the head of the pull request instead of the merge commit. - - run: git checkout HEAD^2 - if: ${{ github.event_name == 'pull_request' }} - - # Ensure a compatible version of dotnet is installed. - # The [Microsoft Security Code Analysis CLI](https://aka.ms/mscadocs) is built with dotnet v3.1.201. - # A version greater than or equal to v3.1.201 of dotnet must be installed on the agent in order to run this action. - # GitHub hosted runners already have a compatible version of dotnet installed and this step may be skipped. - # For self-hosted runners, ensure dotnet version 3.1.201 or later is installed by including this action: - # - name: Install .NET - # uses: actions/setup-dotnet@v1 - # with: - # dotnet-version: '3.1.x' - - # Run open source static analysis tools - - name: Run OSSAR - uses: github/ossar-action@v1 - id: ossar - - # Upload results to the Security tab - - name: Upload OSSAR results - uses: github/codeql-action/upload-sarif@v1 - with: - sarif_file: ${{ steps.ossar.outputs.sarifFile }}