From 5f799014920834997ea2ef6ef31e4d2ef1dad391 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Wed, 29 May 2024 15:20:37 +1000
Subject: [PATCH] test: Adjust for smafa 0.8.0.

---
 .../4.11.22seqs.smafa_naive_index             | Bin 2418 -> 370 bytes
 test/data/22seqs.sdb/otus.sqlite3             | Bin 90112 -> 90112 bytes
 .../4.11.22seqs.smafa_naive_index             | Bin 2418 -> 370 bytes
 .../22seqs.sdb/otus.sqlite3                   | Bin 90112 -> 90112 bytes
 .../4.11.22seqs.gpkg.spkg.smpkg/CONTENTS.json |   2 +-
 .../prefilter.fna.dmnd                        | Bin 3885 -> 3885 bytes
 .../read_taxonomies.sqlite3                   | Bin 856064 -> 856064 bytes
 .../4.11.22seqs.smafa_naive_index             | Bin 304 -> 50 bytes
 .../otus.sqlite3                              | Bin 90112 -> 90112 bytes
 test/test_pipe.py                             |   6 +++---
 10 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/test/data/22seqs.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index b/test/data/22seqs.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index
index 501f2f89eeb33517ed439d86246904360fd49d43..87fa07891f4c9eacd612313b604ae63f7db2baed 100644
GIT binary patch
literal 370
zcmXYt!41P83;-2Gqzu(pCkvJ<nZ8Vv0Sw9@VDZSaBh}FUkU36g+_v78p>fDgD;MTW
z9vg+kNjzT^8bEg3r3++sgD%qd?4V(=XVD|(ad^4Tlo?FKr`)0y{d&uAL-e2VjN=nK
z;Z&oNT?}}tLz=KMHE~!N5<&8qD8x@iN6qGc`mzwT5av>`iyH^#i$`{@bj<8V{L97$
zmbStvI!AXEl>r%z3Eoe>B&ga#RK(QDs&!ALa+b};aF}|r5L@juHOBBZ^=8?qQ>|jF
bVUuls&ArD#Ulk5o?EhLN{LxYOms=iRp!mV0

literal 2418
zcma)4TTTQq4BO?4`=5hDlGusumH~m7)~~o#weQcbkJtN!zuJIEd)@CjG3w6jK69Fe
zp4Dpgam;AFfDV%G$vsV00}||_qtymP+N%*UIb^^i^Ve(XJa?+#ILD2;izG}$lkd?8
zt{1j8PpvTM$YBZ6f1o8vb$j$(?m8=DM@OUMwGgG>>weQ9YKK{sMNryAas#e~|8tN_
z-I7D4l6nO)eQMAdj9s+F$9YwS+wiZ~V$)e^_M5Ad?)Sb<o{L%)BB=fWy-RznAG<^Q
z8DiA)L7lzqsG&2-^R;}h4c#>}R(HAY^>Y>x6u1RbTnuT)x({^@J8<fAm%LFHT;ZS%
zLGP=mimqtAR%5G!uo17@EM#CN8p@53)5;OV+Rzlp6c%aJzTOerv#X|H8cR}Z9K0ad
zti6$A3u}ydEgv=UO=2gZGjrRz;+6BnW$awbVToFVTa<gJSINn7*ZM~ok<IVxG!KKM
z1m;BZwIuFnhndIP%YLatRU$@0t2|h^6sY#PAK-*r9BBLe3BhJ&A_tjyr;Osn5P9AR
H*nGEd7d8i4

diff --git a/test/data/22seqs.sdb/otus.sqlite3 b/test/data/22seqs.sdb/otus.sqlite3
index b0ec5b0f4578822197cb0a1a3ef8c730fbc78315..38d062724e058b539fe44723e0218edd4cc1b818 100644
GIT binary patch
delta 18
ZcmZoTz}j$tbwUzTS$AW~))dA$@c>AD2YLVi

delta 18
ZcmZoTz}j$tbwUzTyi8-t))dA$@c=|N2J`>`

diff --git a/test/data/4.11.22seqs.gpkg.spkg.smpkg/22seqs.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index b/test/data/4.11.22seqs.gpkg.spkg.smpkg/22seqs.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index
index 501f2f89eeb33517ed439d86246904360fd49d43..87fa07891f4c9eacd612313b604ae63f7db2baed 100644
GIT binary patch
literal 370
zcmXYt!41P83;-2Gqzu(pCkvJ<nZ8Vv0Sw9@VDZSaBh}FUkU36g+_v78p>fDgD;MTW
z9vg+kNjzT^8bEg3r3++sgD%qd?4V(=XVD|(ad^4Tlo?FKr`)0y{d&uAL-e2VjN=nK
z;Z&oNT?}}tLz=KMHE~!N5<&8qD8x@iN6qGc`mzwT5av>`iyH^#i$`{@bj<8V{L97$
zmbStvI!AXEl>r%z3Eoe>B&ga#RK(QDs&!ALa+b};aF}|r5L@juHOBBZ^=8?qQ>|jF
bVUuls&ArD#Ulk5o?EhLN{LxYOms=iRp!mV0

literal 2418
zcma)4TTTQq4BO?4`=5hDlGusumH~m7)~~o#weQcbkJtN!zuJIEd)@CjG3w6jK69Fe
zp4Dpgam;AFfDV%G$vsV00}||_qtymP+N%*UIb^^i^Ve(XJa?+#ILD2;izG}$lkd?8
zt{1j8PpvTM$YBZ6f1o8vb$j$(?m8=DM@OUMwGgG>>weQ9YKK{sMNryAas#e~|8tN_
z-I7D4l6nO)eQMAdj9s+F$9YwS+wiZ~V$)e^_M5Ad?)Sb<o{L%)BB=fWy-RznAG<^Q
z8DiA)L7lzqsG&2-^R;}h4c#>}R(HAY^>Y>x6u1RbTnuT)x({^@J8<fAm%LFHT;ZS%
zLGP=mimqtAR%5G!uo17@EM#CN8p@53)5;OV+Rzlp6c%aJzTOerv#X|H8cR}Z9K0ad
zti6$A3u}ydEgv=UO=2gZGjrRz;+6BnW$awbVToFVTa<gJSINn7*ZM~ok<IVxG!KKM
z1m;BZwIuFnhndIP%YLatRU$@0t2|h^6sY#PAK-*r9BBLe3BhJ&A_tjyr;Osn5P9AR
H*nGEd7d8i4

diff --git a/test/data/4.11.22seqs.gpkg.spkg.smpkg/22seqs.sdb/otus.sqlite3 b/test/data/4.11.22seqs.gpkg.spkg.smpkg/22seqs.sdb/otus.sqlite3
index b0ec5b0f4578822197cb0a1a3ef8c730fbc78315..38d062724e058b539fe44723e0218edd4cc1b818 100644
GIT binary patch
delta 18
ZcmZoTz}j$tbwUzTS$AW~))dA$@c>AD2YLVi

delta 18
ZcmZoTz}j$tbwUzTyi8-t))dA$@c=|N2J`>`

diff --git a/test/data/4.11.22seqs.gpkg.spkg.smpkg/CONTENTS.json b/test/data/4.11.22seqs.gpkg.spkg.smpkg/CONTENTS.json
index 5e20774e..ebc0edca 100644
--- a/test/data/4.11.22seqs.gpkg.spkg.smpkg/CONTENTS.json
+++ b/test/data/4.11.22seqs.gpkg.spkg.smpkg/CONTENTS.json
@@ -1 +1 @@
-{"singlem_metapackage_version": 4, "singlem_packages": ["4.11.22seqs.gpkg.spkg"], "prefilter_db_path": "prefilter.fna.dmnd", "nucleotide_sdb": "22seqs.sdb", "sqlite_db_path_key": "read_taxonomies.sqlite3", "taxon_genome_lengths": null}
\ No newline at end of file
+{"singlem_metapackage_version": 5, "singlem_packages": ["4.11.22seqs.gpkg.spkg"], "prefilter_db_path": "prefilter.fna.dmnd", "nucleotide_sdb": "22seqs.sdb", "sqlite_db_path_key": "read_taxonomies.sqlite3", "taxon_genome_lengths": null, "taxonomy_database_name": "custom_taxonomy_database", "taxonomy_database_version": null, "diamond_prefilter_performance_parameters": "--block-size 0.5 --target-indexed -c1", "diamond_taxonomy_assignment_performance_parameters": "--block-size 0.5 --target-indexed -c1", "makeidx_sensitivity_params": null}
\ No newline at end of file
diff --git a/test/data/4.11.22seqs.gpkg.spkg.smpkg/prefilter.fna.dmnd b/test/data/4.11.22seqs.gpkg.spkg.smpkg/prefilter.fna.dmnd
index d0bd67d082776e9acd52946ddbffb7d29ccb1de5..ec4f4b7a756d3e64a7bbcd507f7246fe115751dc 100644
GIT binary patch
delta 18
acmZ20w^oibSK^)Mk{@17i#Kwr@B;us`Uao?

delta 18
acmZ20w^oibSK^)Mk{@17GdFUo@B;us$Oe`G

diff --git a/test/data/4.11.22seqs.gpkg.spkg.smpkg/read_taxonomies.sqlite3 b/test/data/4.11.22seqs.gpkg.spkg.smpkg/read_taxonomies.sqlite3
index dea7aab29f9158ae8a100e075372526c826b1a22..532ee2c44c2e273d6953a5417e86d860b5eae075 100644
GIT binary patch
delta 124
zcmZozVA8O_WI_^OSvN2L4+bW_M+|(A_&0BMRN&#89<YHez4<X;`(r*vAZFVBn2-50
z(?nl^=>e;m*{45P$js9IQIHvkK{P86vjH(X5OV-A=k||+T)*#6bmgD!^OuWzJKHC&
UxAhZ!_}iI^xVJME@%)<$0ErSXjQ{`u

delta 126
zcmZozVA8O_WI_^OybLe@4+bW_M+|(A_&0BMRN&#89<YHez4<X;`(r*vAZFVBn2-50
z6DyM%g8{?za|@Zp+CK_112GE_vjQ<25VHd@2M}{^|0u}y`#uZbV+Q`|j(@qtwzGZW
WdRx!J^ofDL{d*zz_V0x}obv!SZZ8M`

diff --git a/test/data/4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index b/test/data/4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb/nucleotide_indices_smafa_naive/4.11.22seqs.smafa_naive_index
index ccb69ed356ba9e6926318f83aa69fd603bf6f104..3006c771e5883dadcba89d23f51dc66965a42ce0 100644
GIT binary patch
literal 50
zcmZQ#WIfa{aZyLdkp&ze#)Jt=CNQ>4>{vKq!o&rP6IwbOyCyU(<d|?|!IA?_3tKoC
FZ2(|(7yAGJ

literal 304
zcmaiuK@tEU2m-bLKcz>8XwuZ7Lk6-sy3b)|j)%hUt!PK0lq&6K7SIWYuDO=!+logk
bv-<XZ(Pp5s$p;}Q?ovu~VQ;Q8g(Ig~^f>_S

diff --git a/test/data/4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb/otus.sqlite3 b/test/data/4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb/otus.sqlite3
index 96a773d00803130658e00bfef85761d97b7db89f..7b3babfd9e6f1f4381dd21f48f579b0d87553491 100644
GIT binary patch
delta 18
ZcmZoTz}j$tbwUzTS$AW~))dA$@c>AD2YLVi

delta 18
ZcmZoTz}j$tbwUzTyi8-t))dA$@c=|N2J`>`

diff --git a/test/test_pipe.py b/test/test_pipe.py
index 0e9a4d09..fcfefb99 100644
--- a/test/test_pipe.py
+++ b/test/test_pipe.py
@@ -1112,7 +1112,7 @@ def test_smafa_naive_then_diamond_assignment_paired(self):
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg_inseqs.fna'),
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg_inseqs2.fna'),
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg'),
-            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.sdb'),
+            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb'),
         )
         self.assertEqualOtuTable(
             list([line.split("\t") for line in expected]),
@@ -1126,7 +1126,7 @@ def test_smafa_naive_then_diamond_assignment_paired_only_read2_hits(self):
             os.path.join(path_to_data, 'random.fna'), # i.e. no hits
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg_inseqs2.fna'),
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg'),
-            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.sdb'),
+            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb'),
         )
         self.assertEqualOtuTable(
             list([line.split("\t") for line in expected]),
@@ -1140,7 +1140,7 @@ def test_smafa_naive_then_diamond_assignment_paired_only_read1_hits(self):
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg_inseqs2.fna'),
             os.path.join(path_to_data, 'random.fna'), # i.e. no hits
             os.path.join(path_to_data, '4.11.22seqs.gpkg.spkg'),
-            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.sdb'),
+            os.path.join(path_to_data, '4.11.22seqs.paired.manual.json.v5.smafa_naive.sdb'),
         )
         self.assertEqualOtuTable(
             list([line.split("\t") for line in expected]),