Merge remote-tracking branch 'upstream/master' into allow-add-overlap

Author: adamnovak

.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.

test/small/xy.dict

@@ -1,2 +1,3 @@
+@HD	VN:1.5	SO:unknown
 @SQ	SN:x	LN:1001
 @SQ	SN:y	LN:1001

test/small/yx.dict

@@ -1,2 +1,3 @@
+@HD	VN:1.5	SO:unknown
 @SQ	SN:y	LN:1001
 @SQ	SN:x	LN:1001

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"