ignore alt_paths in xg in some tests

Author: glennhickey

test/t/11_vg_paths.t

@@ -14,8 +14,8 @@ vg construct -r small/x.fa -v small/x.vcf.gz > x2.vg
 vg index -x x.xg -G x.gbwt -v small/x.vcf.gz x.vg
 
 # List path/thread names from various input formats
-is "$(vg paths --list -v x2.vg)" "x" "path listing works from vg"
-is "$(vg paths --list -x x.xg)" "x" "path listing works from XG"
+is "$(vg paths --list -v x2.vg | grep -v _alt_)" "x" "path listing works from vg"
+is "$(vg paths --list -x x.xg | grep -v _alt_)" "x" "path listing works from XG"
 is $(vg paths --list -g x.gbwt | wc -l) 2 "thread listing works from GBWT"
 
 # Select threads by name

test/t/30_vg_chunk.t

@@ -42,8 +42,8 @@ is $(vg chunk -x x.xg -r 1 -c 0 | vg view - -j | jq .node | grep id | wc -l) 1 "
 
 # Check that traces work on a GBWT
 is $(vg chunk -x x.xg -G x.gbwt -r 1:1 -c 2 -T | vg view - -j | jq .node | grep id | wc -l) 5 "id chunker traces correct chunk size"
-is "$(vg chunk -x x.xg -r 1:1 -c 2 -T | vg view - -j | jq -c '.path[] | select(.name != "x")' | wc -l)" 0 "chunker extracts no threads from an empty gPBWT"
-is "$(vg chunk -x x.xg -G x.gbwt -r 1:1 -c 2 -T | vg view - -j | jq -c '.path[] | select(.name != "x")' | wc -l)" 2 "chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it"
+is "$(vg chunk -x x.xg -r 1:1 -c 2 -T | vg view - -j | jq -c '.path[] | select(.name != "x")' | grep -v _alt_ | wc -l)" 0 "chunker extracts no threads from an empty gPBWT"
+is "$(vg chunk -x x.xg -G x.gbwt -r 1:1 -c 2 -T | vg view - -j | jq -c '.path[] | select(.name != "x")' | grep -v _alt_ | wc -l)" 2 "chunker extracts 2 local threads from a gBWT with 2 locally distinct threads in it"
 is "$(vg chunk -x x.xg -G x.gbwt -r 1:1 -c 2 -T | vg view - -j | jq -r '.path[] | select(.name == "thread_0") | .mapping | length')" 3 "chunker can extract a partial haplotype from a GBWT"
 
 #check that n-chunking works