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VDB-5980 added an error test for changing readname format mid-file #1079

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VDB-5980 added an error test for changing readname format mid-file #1079

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4 changes: 3 additions & 1 deletion test/loaders/sharq/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ message(RE2_FOUND=${RE2_FOUND})

# test-sharq-writer
add_executable(test-sharq-writer test-sharq-writer.cpp )
add_dependencies(test-sharq-writer RE2 sharq general-loader ) # general-loader for the metadata command line tests
add_dependencies(test-sharq-writer RE2 sharq general-loader ) # general-loader for the metadata command line tests
target_include_directories(test-sharq-writer PUBLIC ${LOCAL_INCDIR} ../../../tools/loaders/sharq)
target_link_libraries(test-sharq-writer ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_READ})
add_test( NAME Test_sharq_writer COMMAND test-sharq-writer WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} )
Expand Down Expand Up @@ -282,6 +282,8 @@ message(RE2_FOUND=${RE2_FOUND})
SharqTestWithMetadata(DbMetaMultipleFiles_input "${IN}r1.fastq ${IN}r2.fastq" ". LOAD")
SharqTestWithMetadata(DbMetaMultipleFiles_output "${IN}r1.fastq ${IN}r2.fastq" "tbl/SEQUENCE QC")

SharqTest(017.readname_format_change 1 "${IN}017.fastq") # error out when readname format changes mid-file

endif()

endif()
1 change: 1 addition & 0 deletions test/loaders/sharq/expected/017.readname_format_change.stderr
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@@ -0,0 +1 @@
[error] [code:70] Input file has data from multiple platforms (2 != 0)
80 changes: 80 additions & 0 deletions test/loaders/sharq/input/017.fastq
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Original file line number Diff line number Diff line change
@@ -0,0 +1,80 @@
@61GN1AAXX:4:1:1054:5268#0/1
AATAAAGATTTTAAATAANTAAAAAAATAGGGTTGGGNNNNNNNNNNNNNNNNNTTTAATAAAATATGTACTAGT
+61GN1AAXX:4:1:1054:5268#0/1
\V\\\PW\T`bb`bX\ZXBXKWVV^LWYY_cc`cYZ]BBBBBBBBBBBBBBBBBTUVVVccc]JbcacacaTY\a
@61GN1AAXX:4:1:1055:1490#0/1
TTAAAATATTTTCTTATTNAATAAAACTTGTTTAAAATNNNANNTANNNNNNNNTTAAAATATAATTCATGTTTT
+61GN1AAXX:4:1:1055:1490#0/1
dYYcddd]ab`bUZPGZVB^YZ][LZP^^```U`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@61GN1AAXX:4:1:1057:13700#0/1
AATATAAATATACCAAATTTCAAAATCACATTGAGGTTNNNAAAGANNNNNNNACCTTTGGATGAATAAATGTCT
+61GN1AAXX:4:1:1057:13700#0/1
`^c^ccYZcccY`cc`\caaccc^JZ]L\b_\ZLYSL_BBBTQTTZBBBBBBBEWOUUT_Y\_YL\_VZa^aaa\
@61GN1AAXX:4:1:1057:20346#0/1
TCGAGCATAACTTTCTCATCGGGACTCCAAATAAAGTGNNNCCGGCNNNNNNNGACAGCTATTTTAGCTGGCTAC
+61GN1AAXX:4:1:1057:20346#0/1
bd\ccddddYdc\\d^dd\d^dadd^ccdcadcaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@61GN1AAXX:4:1:1057:5492#0/1
TACACCATTTTATAAACGAAACAAGTCATGAATCCATANNNCAAGANNNNNNNTTGAAAAAACAATAGTTTACTA
+61GN1AAXX:4:1:1057:5492#0/1
ddLdd^\L^dc^```d\d\dd`d```dddaadadW[VVBBBVZUYVBBBBBBBEZVUVT^dcdbOWbb`d\dcYT
@61GN1AAXX:4:1:1058:11823#0/1
CCAGTACACTATCATCGTCATCGCTACCGCCGCCGCTGNNGAGTTTGNNNNNNAGCTGGTCCTGCCTAGCGGACA
+61GN1AAXX:4:1:1058:11823#0/1
Y^\cddcccccd\LbMUZZ]_aBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@61GN1AAXX:4:1:1059:13146#0/1
AGGCTCTGCAGACAATTTTGCGGGGCTGCAACAATAGANTAACATAANNNNNNGCCAGGAGACACACATAACACA
+61GN1AAXX:4:1:1059:13146#0/1
_ZLZa]```TTaMY^]XT\`^Y``bc^ccYb^``HZ^XBVJUV\H]UBBBBBBYVYUTU\bb\bc^caaY]b`]`
@61GN1AAXX:4:1:1060:10273#0/1
AGTAACAAACAAACACCTCATAAGATGTAGATATTTTAACCTAATTGNNNNNNCTTTTTAATTATGAAAACTATA
+61GN1AAXX:4:1:1060:10273#0/1
acbdbbL``ccc`]Z`b\^cbddd``da^Yb^bY^cScac\cb`TVVBBBBBBUMQTVO`T`\L_\Yb^d\dTdd
@61GN1AAXX:4:1:1060:19532#0/1
AAGTAAGTATACAAAGGCATGCACAAAAGTACTCACGCAAAAGTGCATNNNNNACAAGGATCATGAAAACACAAA
+61GN1AAXX:4:1:1060:19532#0/1
c`cTcccaTTcc\cZ^b\^ccccTcc`cc\ccTcccTccc^\\`UY]YBBBBBVIWUVIc^cc`^c^TaccaYaT
@61GN1AAXX:4:1:1060:9427#0/1
TAATACGTAAATATTTTTAAATTTTAATAATATTTTTCTTTAACTCCNNNNNNTCTCCTCCTTATTTCCAGCCTA
+61GN1AAXX:4:1:1060:9427#0/1
`ad^cccYd^^Lbc`cc]_\\ccaYda^dd\daaddbaddb`dd[^QBBBBBBVY[]S[ad\T\]```TcLc_bd
@E100049707L1C001R00300000007/1
CGATTGCGCGTTAACCTACCAGACTTGAGT
+
FFFFFGFGFGGGGFE<FCFFFGFGGGCEGG
@E100049707L1C001R00300000022/1
CATCATGACCTATGCTCTCCGCTAGCCGGC
+
GGFFFFFDGFGDGFFFGGFGEGG?FFGF@C
@E100049707L1C001R00300000035/1
AATACACGTACACATGTTACAACTCGAGGG
+
ED=ADAA@?BCFFFEF>DF?AEEEFF0BFF
@E100049707L1C001R00300000037/1
AGGTAGTAAAATCCCTAGAGGCTTGCACTC
+
1D;6;>BFDFD9F;>@EF)D+*FFF*5=DD
@E100049707L1C001R00300000044/1
CGGTAACACAACACAGAGACAAGCCAAGGA
+
FGFGGGGGGGGGGGGGGGFGGGGGGGGGGG
@E100049707L1C001R00300000053/1
GGGTATCTCCCTGCAGGAGGAGAGAGAGGA
+
FD@FFFFEFFFEFFGE:FCAF?DFEFFFDD
@E100049707L1C001R00300000054/1
GGGTATCTCCCTGCAGGAGGAGAGAGAGGA
+
F@;CEFFFCFDFFFGEBGE5EFFFFDDEFD
@E100049707L1C001R00300000078/1
AGATCGCCTACTTGCCTACACGGAAGTAAG
+
GFGGGGGGGGGGGGFGGGFGGFDGGGGGFG
@E100049707L1C001R00300000081/1
GTTGGATCCTGTCAGCATGCAGCCAATGGA
+
GFFGFEGGGGGGGFFGFGGGDGFGGGGFDF
@E100049707L1C001R00300000084/1
CACCGAGCATCGATATGTGCGGCAGCGTCA
+
IFGGGGGGGGGGGGGGGGGGFGGFGFGGGG