--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/predict_bam/Genus_species.discrepency.report.txt	Thu Aug 26 06:56:18 2021 +0000
@@ -0,0 +1,142 @@
+Discrepancy Report Results
+
+Summary
+DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"
+DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
+DISC_FEATURE_COUNT:gene: 18 present
+DISC_FEATURE_COUNT:CDS: 18 present
+DISC_FEATURE_COUNT:mRNA: 18 present
+DISC_COUNT_NUCLEOTIDES:4 nucleotide Bioseqs are present
+JOINED_FEATURES:30 features have joined locations.
+NO_ANNOTATION:2 bioseqs have no features
+DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
+FATAL: DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS:2 features have partial ends that do not abut the end of the sequence or a gap, and cannot be extended by 3 or fewer nucleotides to do so
+ONCALLER_COMMENT_PRESENT:4 comment descriptors were found (all same)
+MISSING_GENOMEASSEMBLY_COMMENTS:4 bioseqs are missing GenomeAssembly structured comments
+MOLTYPE_NOT_MRNA:4 molecule types are not set as mRNA.
+TECHNIQUE_NOT_TSA:4 technique are not set as TSA
+MISSING_STRUCTURED_COMMENT:4 sequences do not include structured comments.
+MISSING_PROJECT:22 sequences do not include project.
+DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
+
+
+Detailed Report
+
+DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein"
+
+DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
+DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::4 sources have 'Genus species' for taxname
+DiscRep_ALL:DISC_FEATURE_COUNT::gene: 18 present
+DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 18 present
+DiscRep_ALL:DISC_FEATURE_COUNT::mRNA: 18 present
+DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::4 nucleotide Bioseqs are present
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+
+DiscRep_ALL:JOINED_FEATURES::30 features have joined locations.
+DiscRep_SUB:JOINED_FEATURES::30 features have joined location but no exception
+genome:mRNA	hypothetical protein	(sample4:2126-2199, 2258-3224, 3284->3537)	FUN_000018
+genome:CDS	hypothetical protein	(sample4:2126-2199, 2258-3224, 3284->3537)	FUN_000018
+genome:mRNA	hypothetical protein	(sample:c5802-5797, c5539-4883)	FUN_000002
+genome:CDS	hypothetical protein	(sample:c5802-5797, c5539-4883)	FUN_000002
+genome:mRNA	hypothetical protein	(sample:c10557-10549, c10462-8696)	FUN_000003
+genome:CDS	hypothetical protein	(sample:c10557-10549, c10462-8696)	FUN_000003
+genome:CDS	hypothetical protein	(sample:c15214-15209, c14648-14247)	FUN_000004
+genome:mRNA	hypothetical protein	(sample:c15214-15209, c14648-14247)	FUN_000004
+genome:mRNA	hypothetical protein	(sample:c21705-21700, c21515-19533)	FUN_000005
+genome:CDS	hypothetical protein	(sample:c21705-21700, c21515-19533)	FUN_000005
+genome:CDS	hypothetical protein	(sample:40223-40396, 40659-41193, 41707-42080, 43409-43609, 43678-44130)	FUN_000007
+genome:mRNA	hypothetical protein	(sample:40223-40396, 40659-41193, 41707-42080, 43409-43609, 43678-44130)	FUN_000007
+genome:CDS	hypothetical protein	(sample:c47195-46753, c46330-46214, c46157-45527)	FUN_000008
+genome:mRNA	hypothetical protein	(sample:c47195-46753, c46330-46214, c46157-45527)	FUN_000008
+genome:CDS	hypothetical protein	(sample:c79527-79519, c79068-78685)	FUN_000009
+genome:mRNA	hypothetical protein	(sample:c79527-79519, c79068-78685)	FUN_000009
+genome:mRNA	hypothetical protein	(sample:87202-87207, 88054-88320)	FUN_000010
+genome:CDS	hypothetical protein	(sample:87202-87207, 88054-88320)	FUN_000010
+genome:CDS	hypothetical protein	(sample:133587-134504, 134720-135510, 135569-136284, 137516-137862)	FUN_000011
+genome:mRNA	hypothetical protein	(sample:133587-134504, 134720-135510, 135569-136284, 137516-137862)	FUN_000011
+genome:CDS	hypothetical protein	(sample:144294-144551, 149012-149244, 149367-149588, 149654-149897, 149952-150112, 150174-150248, 151966-152072, 152314-152429, 152496-152751, 153296-153630, 153689-155122, 155789-158975, 159190-164495)	FUN_000012
+genome:mRNA	hypothetical protein	(sample:144294-144551, 149012-149244, 149367-149588, 149654-149897, 149952-150112, 150174-150248, 151966-152072, 152314-152429, 152496-152751, 153296-153630, 153689-155122, 155789-158975, 159190-164495)	FUN_000012
+genome:CDS	hypothetical protein	(sample:167121-168360, 168722-169212)	FUN_000013
+genome:mRNA	hypothetical protein	(sample:167121-168360, 168722-169212)	FUN_000013
+genome:CDS	hypothetical protein	(sample:c178916-178873, c177172-176887, c176824-176699)	FUN_000014
+genome:mRNA	hypothetical protein	(sample:c178916-178873, c177172-176887, c176824-176699)	FUN_000014
+genome:CDS	hypothetical protein	(sample:192004-192067, 193549-193658, 194041-194455, 194518-194669)	FUN_000015
+genome:mRNA	hypothetical protein	(sample:192004-192067, 193549-193658, 194041-194455, 194518-194669)	FUN_000015
+genome:CDS	hypothetical protein	(sample:c210553-210548, c210474-209044)	FUN_000016
+genome:mRNA	hypothetical protein	(sample:c210553-210548, c210474-209044)	FUN_000016
+
+DiscRep_ALL:NO_ANNOTATION::2 bioseqs have no features
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+
+DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
+
+FATAL: DiscRep_ALL:DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS::2 features have partial ends that do not abut the end of the sequence or a gap, and cannot be extended by 3 or fewer nucleotides to do so
+genome:CDS	hypothetical protein	sample:<2331-3254	FUN_000001
+genome:CDS	hypothetical protein	(sample4:2126-2199, 2258-3224, 3284->3537)	FUN_000018
+
+DiscRep_ALL:ONCALLER_COMMENT_PRESENT::4 comment descriptors were found (all same)
+genome:sample:"Annotated using 1.8.7"
+genome:sample2:"Annotated using 1.8.7"
+genome:sample3:"Annotated using 1.8.7"
+genome:sample4:"Annotated using 1.8.7"
+
+DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::4 bioseqs are missing GenomeAssembly structured comments
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+
+DiscRep_ALL:MOLTYPE_NOT_MRNA::4 molecule types are not set as mRNA.
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+
+DiscRep_ALL:TECHNIQUE_NOT_TSA::4 technique are not set as TSA
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+
+DiscRep_ALL:MISSING_STRUCTURED_COMMENT::4 sequences do not include structured comments.
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+
+DiscRep_ALL:MISSING_PROJECT::22 sequences do not include project.
+genome:sample (length 215740)
+genome:ncbi:FUN_000001-T1 (length 307)
+genome:ncbi:FUN_000002-T1 (length 220)
+genome:ncbi:FUN_000003-T1 (length 591)
+genome:ncbi:FUN_000004-T1 (length 135)
+genome:ncbi:FUN_000005-T1 (length 662)
+genome:ncbi:FUN_000006-T1 (length 278)
+genome:ncbi:FUN_000007-T1 (length 578)
+genome:ncbi:FUN_000008-T1 (length 396)
+genome:ncbi:FUN_000009-T1 (length 130)
+genome:ncbi:FUN_000010-T1 (length 90)
+genome:ncbi:FUN_000011-T1 (length 923)
+genome:ncbi:FUN_000012-T1 (length 3977)
+genome:ncbi:FUN_000013-T1 (length 576)
+genome:ncbi:FUN_000014-T1 (length 151)
+genome:ncbi:FUN_000015-T1 (length 246)
+genome:ncbi:FUN_000016-T1 (length 478)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+genome:ncbi:FUN_000017-T1 (length 124)
+genome:ncbi:FUN_000018-T1 (length 432)
+
+DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
+DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
+DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::4 Molinfos are missing field technique
+genome:sample (length 215740)
+genome:sample2 (length 2030)
+genome:sample3 (length 2100)
+genome:sample4 (length 7560)
+