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MANIFEST
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MANIFEST
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Build.PL
Changes
MANIFEST
README
bin/npg_mlwarehouse_fkrepair
bin/npg_run_statuses2mlwarehouse
bin/npg_runs2mlwarehouse
lib/npg_tracking/daemon/fkrepair.pm
lib/npg_warehouse/fk_repair.pm
lib/npg_warehouse/loader/autoqc.pm
lib/npg_warehouse/loader/base.pm
lib/npg_warehouse/loader/fqc.pm
lib/npg_warehouse/loader/npg.pm
lib/npg_warehouse/loader/qc.pm
lib/npg_warehouse/loader/run_status.pm
lib/npg_warehouse/loader/run.pm
lib/st/api/lims/ml_warehouse.pm
lib/st/api/lims/ml_warehouse_fc_cache.pm
lib/st/api/lims/ml_warehouse_auto.pm
t/10-npg_warehouse-fkrepair.t
t/10-npg_warehouse-loader-autoqc.t
t/10-npg_warehouse-loader-fqc.t
t/10-npg_warehouse-loader-npg.t
t/10-npg_warehouse-loader-qc.t
t/10-npg_warehouse-loader-run.t
t/10-npg_warehouse-loader-run_status.t
t/10-st-api-lims-ml_warehouse.t
t/20-npg_warehouse-loader-run.t
t/30-npg_tracking-daemon-fkrepair.t
t/00-critic.t
t/00-distribution.t
t/00-podcoverage.t
t/00-pod.t
t/00-scripts_compile.t
t/perlcriticrc
t/data/fixtures/npg/000-CostCode.yml
t/data/fixtures/npg/000-InstrumentStatusDict.yml
t/data/fixtures/npg/000-RunStatusDict.yml
t/data/fixtures/npg/000-Tag.yml
t/data/fixtures/npg/000-User.yml
t/data/fixtures/npg/100-InstrumentFormat.yml
t/data/fixtures/npg/200-Instrument.yml
t/data/fixtures/npg/300-Run.yml
t/data/fixtures/npg/400-RunLane.yml
t/data/fixtures/npg/400-RunStatus.yml
t/data/fixtures/npg/400-TagRun.yml
t/data/fixtures/npgqc/CacheQuery.yml
t/data/fixtures/npgqc/ClusterDensity.yml
t/data/fixtures/npgqc/Fastqcheck.yml
t/data/fixtures/npgqc/InsertSize.yml
t/data/fixtures/npgqc/MqcLibraryOutcomeDict.yml
t/data/fixtures/npgqc/MqcOutcomeDict.yml
t/data/fixtures/npgqc/QXYield.yml
t/data/fixtures/npgqc/TagMetrics.yml
t/data/fixtures/wh/000-Sample.yml
t/data/fixtures/wh/000-Study.yml
t/data/fixtures/wh/100-IseqFlowcell.yml
t/data/fixtures/wh_npg/200-IseqProductMetric.yml
t/data/fixtures/wh_npg/200-IseqRunLaneMetric.yml
t/data/fixtures_stlims_wh/000-Sample.yml
t/data/fixtures_stlims_wh/000-Study.yml
t/data/fixtures_stlims_wh/100-IseqFlowcell.yml
t/data/fixtures_stlims_wh/100-StudyUser.yml
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.insert_size.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#0.qX_yield.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#1.insert_size.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#2.insert_size.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#3.insert_size.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/lane3/qc/4799_3#3.qX_yield.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.adapter.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.contamination.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.gc_fraction.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.insert_size.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.qX_yield.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.ref_match.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_1.sequence_error.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_3_tag_decode_stats.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.adapter.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.contamination.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.gc_bias.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.gc_fraction.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.insert_size.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.qX_yield.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.ref_match.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4.sequence_error.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_4_tag_decode_stats.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_5_tag_decode_stats.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_6_tag_decode_stats.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_7_tag_decode_stats.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_8.insert_size.json
t/data/runfolders/100330_HS21_4799/Data/Intensities/BAM_basecalls_20141025-143940/no_cal/archive/qc/4799_8_tag_decode_stats.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_1.adapter.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_1.contamination.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_1.gc_fraction.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_1.insert_size.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_1.qX_yield.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_1.sequence_error.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_1_tag_decode_stats.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_2_tag_decode_stats.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_3_tag_decode_stats.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_4.adapter.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_4.contamination.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_4.gc_fraction.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_4.insert_size.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_4.qX_yield.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_4.sequence_error.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_4_tag_decode_stats.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_5_tag_decode_stats.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_6_tag_decode_stats.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_7_tag_decode_stats.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_8.insert_size.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4333_8_tag_decode_stats.json
t/data/runfolders/100330_IL21_4333/Data/Intensities/BAM_basecalls_20141021-094321/no_cal/archive/qc/4523_4.gc_bias.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#0_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#1.genotype.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#1.pulldown_metrics.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#168_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#1_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#2.pulldown_metrics.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#2_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#3_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#4_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#5_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#6_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#7_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/lane3/qc/6624_3#8_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_1.tag_metrics.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_1_1-6624_1_2_phix_split_stats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_1_phix_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_2.tag_metrics.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_2_1-6624_2_2_phix_split_stats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_2_phix_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_2_tag_decode_stats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_3_1-6624_3_2_phix_split_stats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_3_phix_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_3_tag_decode_stats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_4.tag_metrics.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_4_1-6624_4_2_phix_split_stats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_4_phix_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_5.tag_metrics.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_5_1-6624_5_2_phix_split_stats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_5_phix_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_6_1-6624_6_2_phix_split_stats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_6_phix_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_7_1-6624_7_2_phix_split_stats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_7_phix_bam_flagstats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_8_1-6624_8_2_phix_split_stats.json
t/data/runfolders/110731_HS17_06624_A_B00T5ACXX/Data/Intensities/BAM_basecalls_20110811-145428/no_cal/archive/qc/6624_8_phix_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_human#0_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_human#1_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_human#2_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_human#3_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_human#4_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_nonhuman#0_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_nonhuman#1_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_nonhuman#2_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_nonhuman#3_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_nonhuman#4_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_xahuman#5_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/lane2/qc/6642_2_yhuman#6_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/qc/6642_4_verify_bam_id.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/qc/6642_1_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/qc/6642_2_1-6642_2_2_human_split_stats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/qc/6642_3_bam_flagstats.json
t/data/runfolders/110804_HS22_06642_A_B020JACXX/Data/Intensities/PB_basecalls_20110813-160456/no_cal/archive/qc/6642_4_bam_flagstats.json