fix rgfa tests post merge

vgteam · Oct 6, 2023 · 9df2a05 · 9df2a05 · adamnovak · Oct 9, 2023
1 parent 0ad32a2
commit 9df2a05
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Showing 2 changed files with 2 additions and 8 deletions.
diff --git a/src/algorithms/gfa_to_handle.cpp b/src/algorithms/gfa_to_handle.cpp
@@ -674,10 +674,6 @@ tuple<string, size_t, string, pair<int64_t, int64_t>, GFAParser::chars_t, GFAPar
 
     // Grab the haplotype number
     int64_t haplotype_number = take_number(cursor, end, -1, "parsing haplotype number");
-    if (haplotype_number == -1) {
-        // This field is required
-        throw GFAFormatError("Missing haplotype number in W line", cursor);
-    }
     take_tab(cursor, end, "parsing end of haplotype number");
 
     // Grab the sequence/contig/locus name

diff --git a/test/t/48_vg_convert.t b/test/t/48_vg_convert.t
@@ -404,15 +404,13 @@ is "${?}" "0" "GFA -> HashGraph -> GFA conversion preserves path metadata"
 
 # We can't do rGFA to GBZ directly until the GBWTGraph GFA parser learns to read tags
 # rGFA to HashGraph to GBZ to GFA
-# todo: would be great if gbz could preserve the NO_HAPLOTYPE
-#       gbz also strips the end of the subrange
-vg paths -M -x graphs/rgfa_with_reference.rgfa | sed -e 's/NO_HAPLOTYPE/0/g' -e 's/_rGFA_#/_rGFA_#0#/g' -e 's/-2//g' -e 's/-8//g' |  sort >paths.truth.txt
+vg paths -M -x graphs/rgfa_with_reference.rgfa | sed -e 's/-2//g' -e 's/-8//g' |  sort >paths.truth.txt
 vg convert -a graphs/rgfa_with_reference.rgfa > rgfa_with_reference.hg
 vg gbwt -x rgfa_with_reference.hg -E --gbz-format -g rgfa_with_reference.gbz
 vg paths -M -x rgfa_with_reference.gbz | sort >paths.gbz.txt
 cmp paths.gbz.txt paths.truth.txt
 is "${?}" "0" "rGFA -> HashGraph -> GBZ conversion preserves path metadata"
-vg paths -M -x graphs/rgfa_with_reference.rgfa | sed -e 's/NO_HAPLOTYPE/0/g' -e 's/_rGFA_#/_rGFA_#0#/g' |  sort >paths.truth.txt
+vg paths -M -x graphs/rgfa_with_reference.rgfa |  sort >paths.truth.txt
 vg convert -f rgfa_with_reference.gbz >extracted.gfa
 vg paths -M -x extracted.gfa | sort >paths.gfa.txt
 cmp paths.gfa.txt paths.truth.txt