File Changes for markd

v245_preview2 to v245_base (2010-12-21 to 2011-01-04) v245

• src/hg/genePredHisto/makefile
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    hg/utils tests were not automatically run
• src/hg/genePredHisto/tests/makefile
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    hg/utils tests were not automatically run
• src/hg/lib/hgRelate.c
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    removed comment that is no longer true
• src/hg/makefile
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    moved to programs to hg/utils, fixed build of distributed utilities
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    hg/utils tests were not automatically run
• src/hg/overlapSelect/chromAnn.c
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/chromAnn.h
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/chromAnnMap.c
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/chromAnnMap.h
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/coordCols.c
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/coordCols.h
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/makefile
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/overlapSelect.c
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/rowReader.c
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/rowReader.h
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/selectTable.c
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/selectTable.h
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_nonover_NM_015110bed.bed
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_nonover_NM_015110bed_split.bed
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_nonover_NM_015110gp.bed
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_nonover_NM_015110gp.drop.bed
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_over_NM_015110bed.bed
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_over_NM_015110bedIdOutput.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_over_NM_015110bedMerge.bed
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_over_NM_015110bedStatsOutput.stats
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_over_NM_015110bedStatsOutputAll.stats
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_over_NM_015110bed_split.bed
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_over_NM_015110gp.bed
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_over_NM_015110gp.drop.bed
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_over_bedStatsOutputBoth.stats
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_threshold_ceil_only.bed
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/bed_threshold_ceil_only_no.bed
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/cdsOverlapCdsCds.gp
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/cdsOverlapCdsExon.gp
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/cdsOverlapExonCds.gp
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/cds_id_out_gp.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/chain_nonover_NM_001206bed.chain
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/chain_over_NM_015110gp.chain
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/chain_over_NM_015110gp.drop.chain
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/chain_over_chain_stats.stats
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/chain_over_chainq_stats.stats
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/chainq_over_chain_stats.stats
  • lines changed 39, context: html, text, full: html, text
    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/chainq_over_chainq_stats.stats
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/colExclude.cluster
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/colSelect.cluster
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/colSelectMerge.cluster
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/colSelectStrand.cluster
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/colStats.cluster
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/exludeself_nonover_mrna1.psl
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/exludeself_nonover_mrna2.psl
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/exludeself_over_mrna1.psl
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/exludeself_over_mrna2.psl
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregate100.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregate100Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregate75.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregate75Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregate95.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregate95Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregateCds100.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregateCds100Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregateCds75.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregateCds75Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregateCds95.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregateCds95Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_aggregateStats.stats
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarity100.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarity100Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarity75.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarity75Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarity95.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarity95Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarityCds100.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarityCds100Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarityCds75.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarityCds75Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarityCds95.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_similarityCds95Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_threshold100.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_threshold100Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_threshold75.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_threshold75Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_threshold95.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_threshold95Rev.ids
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• src/hg/overlapSelect/tests/expected/gp_gp_thresholdCds100.ids
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• src/hg/overlapSelect/tests/expected/gp_gp_thresholdCds100Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_thresholdCds75.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_thresholdCds75Rev.ids
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_gp_thresholdCds95.ids
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• src/hg/overlapSelect/tests/expected/gp_gp_thresholdCds95Rev.ids
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• src/hg/overlapSelect/tests/expected/gp_psl_prot80.psl
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/gp_psl_protStats.stats
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    moved to programs to hg/utils, fixed build of distributed utilities
• src/hg/overlapSelect/tests/expected/idMatchSimple.gp
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• src/hg/overlapSelect/tests/expected/idMatchSimpleNon.gp
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• src/hg/overlapSelect/tests/expected/name2EmptyTest.gp
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• src/hg/overlapSelect/tests/expected/noCdsSelect.gp
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• src/hg/overlapSelect/tests/expected/noCdsSelectNoOver.gp
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• src/hg/overlapSelect/tests/expected/orthoStrandTest.stats
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• src/hg/overlapSelect/tests/expected/overlapBases2100.bed
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• src/hg/overlapSelect/tests/expected/overlapBases250.bed
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• src/hg/overlapSelect/tests/expected/overlapBases3000.bed
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• src/hg/overlapSelect/tests/expected/psl_gp_aggregate.drop.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_aggregate.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_aggregateStatsAll.stats
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• src/hg/overlapSelect/tests/expected/psl_gp_non_aggregate.drop.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_non_aggregate.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_non_similarity.drop.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_non_similarity.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_non_threshold.drop.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_non_threshold.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_prot80.gp
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• src/hg/overlapSelect/tests/expected/psl_gp_protStats.stats
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• src/hg/overlapSelect/tests/expected/psl_gp_similarity.drop.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_similarity.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_similarity_ceil.drop.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_similarity_ceil.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_threshold.drop.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_threshold.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_threshold_ceil.drop.psl
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• src/hg/overlapSelect/tests/expected/psl_gp_threshold_ceil.psl
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• src/hg/overlapSelect/tests/expected/psl_idMatch.drop.psl
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• src/hg/overlapSelect/tests/expected/psl_idMatch.psl
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• src/hg/overlapSelect/tests/expected/psl_idMatch_non.drop.psl
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• src/hg/overlapSelect/tests/expected/psl_idMatch_non.psl
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• src/hg/overlapSelect/tests/expected/psl_nonover_NM_001206bed.psl
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• src/hg/overlapSelect/tests/expected/psl_nonover_NM_001206gp.psl
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• src/hg/overlapSelect/tests/expected/psl_nonover_NM_015110bed.psl
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• src/hg/overlapSelect/tests/expected/psl_nonover_NM_015110bed_split.psl
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• src/hg/overlapSelect/tests/expected/psl_nonover_NM_015110gp.drop.psl
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• src/hg/overlapSelect/tests/expected/psl_nonover_NM_015110gp.psl
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• src/hg/overlapSelect/tests/expected/psl_over_NM_001206bed.psl
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• src/hg/overlapSelect/tests/expected/psl_over_NM_001206bedIdOutput.ids
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• src/hg/overlapSelect/tests/expected/psl_over_NM_001206bedMerge.psl
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• src/hg/overlapSelect/tests/expected/psl_over_NM_001206bedStatsOutput.stats
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