diff --git a/.travis.yml b/.travis.yml index f16ccc03771..d3b91515b41 100644 --- a/.travis.yml +++ b/.travis.yml @@ -34,7 +34,7 @@ before_install: # inability to link it as an error and fail the command. You can --force a link step, but # I don't see a way to tell it to not replace things that exist and also not fail. - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew bundle --verbose || true; fi - - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew link --overwrite python@3.8; fi + - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew link --overwrite python@3.9 || brew link --overwrite python@3.8 || true; fi # Try installing gcc6 twice in case of errors like this: # Error: HOMEBREW_LOGS was not exported! # Please don't worry, you likely hit a bug auto-updating from an old version. diff --git a/test/small/xy.dict b/test/small/xy.dict index 290dd016ef3..5e3bc542c35 100644 --- a/test/small/xy.dict +++ b/test/small/xy.dict @@ -1,2 +1,3 @@ +@HD VN:1.5 SO:unknown @SQ SN:x LN:1001 @SQ SN:y LN:1001 diff --git a/test/small/yx.dict b/test/small/yx.dict index 0ce4baac457..529e4ac19e4 100644 --- a/test/small/yx.dict +++ b/test/small/yx.dict @@ -1,2 +1,3 @@ +@HD VN:1.5 SO:unknown @SQ SN:y LN:1001 @SQ SN:x LN:1001 diff --git a/test/t/50_vg_giraffe.t b/test/t/50_vg_giraffe.t index 480a810d9e7..adbb4afb04c 100644 --- a/test/t/50_vg_giraffe.t +++ b/test/t/50_vg_giraffe.t @@ -70,8 +70,8 @@ rm -f x.vg x.gbwt x.gg x.snarls x.min x.dist x.gg x.fa x.fa.fai x.vcf.gz x.vcf.g cp small/xy.fa . cp small/xy.vcf.gz . cp small/xy.vcf.gz.tbi . -vg giraffe xy.fa xy.vcf.gz -f small/x.fa_1.fastq -o SAM --ref-paths small/yx.dict | grep "@SQ" > surjected-yx.dict -vg giraffe xy.fa xy.vcf.gz -f small/x.fa_1.fastq -o SAM --ref-paths small/xy.dict | grep "@SQ" > surjected-xy.dict +vg giraffe xy.fa xy.vcf.gz -f small/x.fa_1.fastq -o SAM --ref-paths small/yx.dict | grep -E "^@(SQ|HD)" > surjected-yx.dict +vg giraffe xy.fa xy.vcf.gz -f small/x.fa_1.fastq -o SAM --ref-paths small/xy.dict | grep -E "^@(SQ|HD)" > surjected-xy.dict diff surjected-yx.dict small/yx.dict is "${?}" "0" "surjecting with a sequence dictionary in non-sorted order produces headers in non-sorted order"