Java Class

SAMFlag

in htsjdk.samtools

Fully qualified name:	htsjdk.samtools.SAMFlag
Containing JAR files:	Show pre-releases [JAR] htsjdk-5.0.0.jar in com/github/samtools/htsjdk/5.0.0 [JAR] htsjdk-5.0.0-all.jar in com/github/samtools/htsjdk/5.0.0 [JAR] htsjdk-2.20.3.jar in com/github/samtools/htsjdk/2.20.3 [JAR] htsjdk-2.15.1.jar in com/github/samtools/htsjdk/2.15.1 [JAR] htsjdk-2.15.0.jar in com/github/samtools/htsjdk/2.15.0 [JAR] htsjdk-2.14.3.jar in com/github/samtools/htsjdk/2.14.3 [JAR] htsjdk-2.14.2.jar in com/github/samtools/htsjdk/2.14.2 [JAR] htsjdk-2.14.1.jar in com/github/samtools/htsjdk/2.14.1 [JAR] htsjdk-2.14.0.jar in com/github/samtools/htsjdk/2.14.0 [JAR] htsjdk-2.13.2.jar in com/github/samtools/htsjdk/2.13.2

	[JAR] htsjdk-2.13.1.jar in com/github/samtools/htsjdk/2.13.1 [JAR] htsjdk-2.13.0.jar in com/github/samtools/htsjdk/2.13.0 [JAR] htsjdk-2.12.0.jar in com/github/samtools/htsjdk/2.12.0 [JAR] htsjdk-2.11.0.jar in com/github/samtools/htsjdk/2.11.0 [JAR] htsjdk-2.10.1.jar in com/github/samtools/htsjdk/2.10.1 [JAR] htsjdk-2.10.0.jar in com/github/samtools/htsjdk/2.10.0 [JAR] htsjdk-2.9.1.jar in com/github/samtools/htsjdk/2.9.1 [JAR] htsjdk-2.9.0.jar in com/github/samtools/htsjdk/2.9.0 [JAR] htsjdk-2.8.1.jar in com/github/samtools/htsjdk/2.8.1 [JAR] htsjdk-2.8.0.jar in com/github/samtools/htsjdk/2.8.0 [JAR] htsjdk-2.7.0.jar in com/github/samtools/htsjdk/2.7.0 [JAR] htsjdk-2.6.1.jar in com/github/samtools/htsjdk/2.6.1 [JAR] htsjdk-2.6.0.jar in com/github/samtools/htsjdk/2.6.0 [JAR] htsjdk-2.5.1.jar in com/github/samtools/htsjdk/2.5.1 [JAR] htsjdk-2.5.0.jar in com/github/samtools/htsjdk/2.5.0 [JAR] htsjdk-2.4.1.jar in com/github/samtools/htsjdk/2.4.1 [JAR] htsjdk-2.4.0.jar in com/github/samtools/htsjdk/2.4.0 [JAR] htsjdk-2.3.0.jar in com/github/samtools/htsjdk/2.3.0 [JAR] htsjdk-2.2.4.jar in com/github/samtools/htsjdk/2.2.4 [JAR] htsjdk-2.2.3.jar in com/github/samtools/htsjdk/2.2.3 [JAR] htsjdk-2.2.2.jar in com/github/samtools/htsjdk/2.2.2 [JAR] htsjdk-2.2.1.jar in com/github/samtools/htsjdk/2.2.1 [JAR] htsjdk-2.2.0.jar in com/github/samtools/htsjdk/2.2.0 [JAR] htsjdk-2.1.1.jar in com/github/samtools/htsjdk/2.1.1 [JAR] htsjdk-2.1.0.jar in com/github/samtools/htsjdk/2.1.0 [JAR] htsjdk-2.0.1.jar in com/github/samtools/htsjdk/2.0.1 [JAR] htsjdk-2.0.0.jar in com/github/samtools/htsjdk/2.0.0 [JAR] htsjdk-1.143.jar in com/github/samtools/htsjdk/1.143 [JAR] htsjdk-1.142.jar in com/github/samtools/htsjdk/1.142 [JAR] htsjdk-1.141.jar in com/github/samtools/htsjdk/1.141 [JAR] htsjdk-1.140.jar in com/github/samtools/htsjdk/1.140 [JAR] htsjdk-1.139.jar in com/github/samtools/htsjdk/1.139 [JAR] htsjdk-1.138.jar in com/github/samtools/htsjdk/1.138 [JAR] htsjdk-1.137.jar in com/github/samtools/htsjdk/1.137 [JAR] variant-spark_2.11-0.5.0-a0-dev5-all.jar in au/csiro/aehrc/variant-spark/variant-spark_2.11/0.5.0-a0-dev5 [JAR] variant-spark_2.11-0.4.0-all.jar in au/csiro/aehrc/variant-spark/variant-spark_2.11/0.4.0 [JAR] variant-spark_2.11-0.1.0-all.jar in au/csiro/aehrc/variant-spark/variant-spark_2.11/0.1.0 [JAR] variant-spark_2.12-0.5.5-all.jar in au/csiro/aehrc/variant-spark/variant-spark_2.12/0.5.5 [JAR] picard-3.5.0-all.jar in com/github/broadinstitute/picard/3.5.0 [JAR] adam-examples_2.10-0.22.0.jar in com/github/heuermh/adamexamples/adam-examples_2.10/0.22.0 [JAR] adam-examples_2.10-0.19.0.jar in com/github/heuermh/adamexamples/adam-examples_2.10/0.19.0 [JAR] adam-examples_2.10-0.18.2.jar in com/github/heuermh/adamexamples/adam-examples_2.10/0.18.2 [JAR] adam-examples_2.11-0.30.0.jar in com/github/heuermh/adamexamples/adam-examples_2.11/0.30.0 [JAR] adam-examples_2.11-0.23.0.jar in com/github/heuermh/adamexamples/adam-examples_2.11/0.23.0 [JAR] adam-examples_2.11-0.19.0.jar in com/github/heuermh/adamexamples/adam-examples_2.11/0.19.0 [JAR] adam-examples_2.11-0.18.2.jar in com/github/heuermh/adamexamples/adam-examples_2.11/0.18.2 [JAR] adam-examples_2.12-1.0.jar in com/github/heuermh/adamexamples/adam-examples_2.12/1.0 [JAR] adam-gfa_2.11-0.5.0.jar in com/github/heuermh/adamgfa/adam-gfa_2.11/0.5.0 [JAR] adam-gfa_2.12-0.8.0.jar in com/github/heuermh/adamgfa/adam-gfa_2.12/0.8.0 [JAR] EmbedSingularityExample-0.13.0-shaded.jar in com/hubspot/EmbedSingularityExample/0.13.0 [JAR] SingularityService-0.13.0-shaded.jar in com/hubspot/SingularityService/0.13.0 [JAR] genomicsdb-0.10.2-proto-3.0.0-beta-1+90dad1af8ce0e4d-jar-with-dependencies.jar in com/intel/genomicsdb/0.10.2-proto-3.0.0-beta-1+90dad1af8ce0e4d [JAR] genomicsdb-0.9.2-proto-3.0.0-beta-1+uuid-static-jar-with-dependencies.jar in com/intel/genomicsdb/0.9.2-proto-3.0.0-beta-1+uuid-static [JAR] genomicsdb-0.9.2-proto-3.0.0-beta-1+f222734d-jar-with-dependencies.jar in com/intel/genomicsdb/0.9.2-proto-3.0.0-beta-1+f222734d [JAR] genomicsdb-0.9.2-proto-3.0.0-beta-1+ed318f7e815-jar-with-dependencies.jar in com/intel/genomicsdb/0.9.2-proto-3.0.0-beta-1+ed318f7e815 [JAR] genomicsdb-0.9.2-proto-3.0.0-beta-1+ebdd81d70ca-jar-with-dependencies.jar in com/intel/genomicsdb/0.9.2-proto-3.0.0-beta-1+ebdd81d70ca [JAR] genomicsdb-0.9.2-proto-3.0.0-beta-1+e071855938-jar-with-dependencies.jar in com/intel/genomicsdb/0.9.2-proto-3.0.0-beta-1+e071855938 [JAR] genomicsdb-0.9.2-proto-3.0.0-beta-1+d8f149eef716-jar-with-dependencies.jar in com/intel/genomicsdb/0.9.2-proto-3.0.0-beta-1+d8f149eef716 [JAR] genomicsdb-0.9.2-proto-3.0.0-beta-1+b825ffa6eb47a-jar-with-dependencies.jar in com/intel/genomicsdb/0.9.2-proto-3.0.0-beta-1+b825ffa6eb47a [JAR] genomicsdb-0.9.2-proto-3.0.0-beta-1+023fbf70-jar-with-dependencies.jar in com/intel/genomicsdb/0.9.2-proto-3.0.0-beta-1+023fbf70 [JAR] genomicsdb-0.9.2-proto-3.0.0-beta-1+6d8f87d9e-jar-with-dependencies.jar in com/intel/genomicsdb/0.9.2-proto-3.0.0-beta-1+6d8f87d9e [JAR] genomicsdb-0.9.2-proto-3.0.0-beta-1+3e2aa-jar-with-dependencies.jar in com/intel/genomicsdb/0.9.2-proto-3.0.0-beta-1+3e2aa [JAR] genomicsdb-0.9.1-proto-3.0.0-beta-1+uuid-static-jar-with-dependencies.jar in com/intel/genomicsdb/0.9.1-proto-3.0.0-beta-1+uuid-static [JAR] genomicsdb-0.8.1-proto-3.0.0-beta-1+uuid-static-jar-with-dependencies.jar in com/intel/genomicsdb/0.8.1-proto-3.0.0-beta-1+uuid-static [JAR] genomicsdb-0.8.1-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.8.1-proto-3.0.0-beta-1 [JAR] genomicsdb-0.8.1-ebca6e68-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.8.1-ebca6e68-proto-3.0.0-beta-1 [JAR] genomicsdb-0.8.1-caa697df9-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.8.1-caa697df9-proto-3.0.0-beta-1 [JAR] genomicsdb-0.8.1-a88557700-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.8.1-a88557700-proto-3.0.0-beta-1 [JAR] genomicsdb-0.8.1-a666036-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.8.1-a666036-proto-3.0.0-beta-1 [JAR] genomicsdb-0.8.0-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.8.0-proto-3.0.0-beta-1 [JAR] genomicsdb-0.7.0-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.7.0-proto-3.0.0-beta-1 [JAR] genomicsdb-0.6.4-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.6.4-proto-3.0.0-beta-1 [JAR] genomicsdb-0.6.3-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.6.3-proto-3.0.0-beta-1 [JAR] genomicsdb-0.6.2-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.6.2-proto-3.0.0-beta-1 [JAR] genomicsdb-0.6.1-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.6.1-proto-3.0.0-beta-1 [JAR] genomicsdb-0.6.0-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.6.0-proto-3.0.0-beta-1 [JAR] genomicsdb-0.5.0-proto-3.0.0-beta-1-jar-with-dependencies.jar in com/intel/genomicsdb/0.5.0-proto-3.0.0-beta-1 [JAR] genomicsdb-0.4.0-jar-with-dependencies.jar in com/intel/genomicsdb/0.4.0 [JAR] genomicsdb-gatk4-0.4.0-jar-with-dependencies.jar in com/intel/genomicsdb-gatk4/0.4.0 [JAR] genomicsdb-gatk4-0.4.0-dependencies.jar in com/intel/genomicsdb-gatk4/0.4.0 [JAR] jannovar-cli-0.41.jar in de/charite/compbio/jannovar-cli/0.41 [JAR] jannovar-cli-0.33.jar in de/charite/compbio/jannovar-cli/0.33 [JAR] jannovar-cli-0.25.jar in de/charite/compbio/jannovar-cli/0.25 [JAR] jannovar-cli-0.24.jar in de/charite/compbio/jannovar-cli/0.24 [JAR] jannovar-cli-0.23.jar in de/charite/compbio/jannovar-cli/0.23 [JAR] jannovar-cli-0.22.jar in de/charite/compbio/jannovar-cli/0.22 [JAR] jannovar-cli-0.21.jar in de/charite/compbio/jannovar-cli/0.21 [JAR] jannovar-cli-0.20.jar in de/charite/compbio/jannovar-cli/0.20 [JAR] jannovar-cli-0.19.jar in de/charite/compbio/jannovar-cli/0.19 [JAR] jannovar-cli-0.18.jar in de/charite/compbio/jannovar-cli/0.18 [JAR] jannovar-cli-0.17.jar in de/charite/compbio/jannovar-cli/0.17 [JAR] jannovar-cli-0.16.jar in de/charite/compbio/jannovar-cli/0.16 [JAR] jannovar-cli-0.15.jar in de/charite/compbio/jannovar-cli/0.15 [JAR] jannovar-filter-0.16.jar in de/charite/compbio/jannovar-filter/0.16 [JAR] jannovar-filter-0.15.jar in de/charite/compbio/jannovar-filter/0.15 [JAR] jped-cli-0.16.jar in de/charite/compbio/jped-cli/0.16 [JAR] jped-cli-0.15.jar in de/charite/compbio/jped-cli/0.15 [JAR] lite-bfx-spark-0.0.0-main-900fba4.jar in io/github/peterdowdy/lite-bfx-spark/0.0.0-main-900fba4 [JAR] lite-bfx-spark-scala_2.13-0.0.0-main-900fba4.jar in io/github/peterdowdy/lite-bfx-spark-scala_2.13/0.0.0-main-900fba4 [JAR] tassel-5.2.98-jar-with-dependencies.jar in net/maizegenetics/tassel/5.2.98 [JAR] adam-assembly-spark2_2.10-0.22.0.jar in org/bdgenomics/adam/adam-assembly-spark2_2.10/0.22.0 [JAR] adam-assembly-spark2_2.10-0.21.0.jar in org/bdgenomics/adam/adam-assembly-spark2_2.10/0.21.0 [JAR] adam-assembly-spark2_2.10-0.20.0.jar in org/bdgenomics/adam/adam-assembly-spark2_2.10/0.20.0 [JAR] adam-assembly-spark2_2.11-0.33.0.jar in org/bdgenomics/adam/adam-assembly-spark2_2.11/0.33.0 [JAR] adam-assembly-spark2_2.11-0.24.0.jar in org/bdgenomics/adam/adam-assembly-spark2_2.11/0.24.0 [JAR] adam-assembly-spark2_2.11-0.23.0.jar in org/bdgenomics/adam/adam-assembly-spark2_2.11/0.23.0 [JAR] adam-assembly-spark2_2.11-0.22.0.jar in org/bdgenomics/adam/adam-assembly-spark2_2.11/0.22.0 [JAR] adam-assembly-spark2_2.11-0.21.0.jar in org/bdgenomics/adam/adam-assembly-spark2_2.11/0.21.0 [JAR] adam-assembly-spark2_2.11-0.20.0.jar in org/bdgenomics/adam/adam-assembly-spark2_2.11/0.20.0 [JAR] adam-assembly-spark2_2.12-0.33.0.jar in org/bdgenomics/adam/adam-assembly-spark2_2.12/0.33.0 [JAR] adam-assembly-spark3_2.12-1.0.1.jar in org/bdgenomics/adam/adam-assembly-spark3_2.12/1.0.1 [JAR] adam-assembly_2.10-0.23.0.jar in org/bdgenomics/adam/adam-assembly_2.10/0.23.0 [JAR] adam-assembly_2.10-0.22.0.jar in org/bdgenomics/adam/adam-assembly_2.10/0.22.0 [JAR] adam-assembly_2.10-0.21.0.jar in org/bdgenomics/adam/adam-assembly_2.10/0.21.0 [JAR] adam-assembly_2.10-0.20.0.jar in org/bdgenomics/adam/adam-assembly_2.10/0.20.0 [JAR] adam-assembly_2.11-0.23.0.jar in org/bdgenomics/adam/adam-assembly_2.11/0.23.0 [JAR] adam-assembly_2.11-0.22.0.jar in org/bdgenomics/adam/adam-assembly_2.11/0.22.0 [JAR] adam-assembly_2.11-0.21.0.jar in org/bdgenomics/adam/adam-assembly_2.11/0.21.0 [JAR] adam-assembly_2.11-0.20.0.jar in org/bdgenomics/adam/adam-assembly_2.11/0.20.0 [JAR] adam-cli_2.10-0.19.0.jar in org/bdgenomics/adam/adam-cli_2.10/0.19.0 [JAR] adam-cli_2.10-0.18.2.jar in org/bdgenomics/adam/adam-cli_2.10/0.18.2 [JAR] adam-cli_2.11-0.19.0.jar in org/bdgenomics/adam/adam-cli_2.11/0.19.0 [JAR] adam-cli_2.11-0.18.2.jar in org/bdgenomics/adam/adam-cli_2.11/0.18.2 [JAR] avocado-cli_2.10-0.1.0.jar in org/bdgenomics/avocado/avocado-cli_2.10/0.1.0 [JAR] avocado-cli_2.11-0.1.0.jar in org/bdgenomics/avocado/avocado-cli_2.11/0.1.0 [JAR] cannoli-assembly-spark2_2.10-0.1.0.jar in org/bdgenomics/cannoli/cannoli-assembly-spark2_2.10/0.1.0 [JAR] cannoli-assembly-spark2_2.11-0.11.1.jar in org/bdgenomics/cannoli/cannoli-assembly-spark2_2.11/0.11.1 [JAR] cannoli-assembly-spark2_2.11-0.2.0.jar in org/bdgenomics/cannoli/cannoli-assembly-spark2_2.11/0.2.0 [JAR] cannoli-assembly-spark2_2.11-0.1.0.jar in org/bdgenomics/cannoli/cannoli-assembly-spark2_2.11/0.1.0 [JAR] cannoli-assembly-spark2_2.12-0.11.1.jar in org/bdgenomics/cannoli/cannoli-assembly-spark2_2.12/0.11.1 [JAR] cannoli-assembly-spark3_2.12-1.0.1.jar in org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/1.0.1 [JAR] cannoli-assembly_2.10-0.1.0.jar in org/bdgenomics/cannoli/cannoli-assembly_2.10/0.1.0 [JAR] cannoli-assembly_2.11-0.1.0.jar in org/bdgenomics/cannoli/cannoli-assembly_2.11/0.1.0 [JAR] deca-cli_2.11-0.2.0.jar in org/bdgenomics/deca/deca-cli_2.11/0.2.0 [JAR] deca-cli_2.11-0.1.0.jar in org/bdgenomics/deca/deca-cli_2.11/0.1.0 [JAR] mango-assembly-0.0.5.jar in org/bdgenomics/mango/mango-assembly/0.0.5 [JAR] mango-assembly-0.0.1.jar in org/bdgenomics/mango/mango-assembly/0.0.1 [JAR] mango-assembly-0.0.1-rc1.jar in org/bdgenomics/mango/mango-assembly/0.0.1-rc1 [JAR] mango-cli-0.0.1.jar in org/bdgenomics/mango/mango-cli/0.0.1 [JAR] mango-cli-0.0.1-rc1.jar in org/bdgenomics/mango/mango-cli/0.0.1-rc1 [JAR] mango-core-0.0.1.jar in org/bdgenomics/mango/mango-core/0.0.1 [JAR] mango-core-0.0.1-rc1.jar in org/bdgenomics/mango/mango-core/0.0.1-rc1 [JAR] quinine-cli_2.10-0.0.2.jar in org/bdgenomics/quinine/quinine-cli_2.10/0.0.2 [JAR] quinine-cli_2.11-0.0.2.jar in org/bdgenomics/quinine/quinine-cli_2.11/0.0.2 [JAR] biokotlin-1.0.0-all.jar in org/biokotlin/biokotlin/1.0.0 [JAR] tassel-5.2.97-all.jar in org/btmonier/tassel/5.2.97 [JAR] genotype-1.3.2-bin-native.jar in org/campagnelab/dl/genotype/1.3.2 [JAR] somatic-1.3.2-bin-native.jar in org/campagnelab/dl/somatic/1.3.2 [JAR] dsh-bio-adam-2.2.jar in org/dishevelled/dsh-bio-adam/2.2 [JAR] dsh-bio-adam-1.0.1.jar in org/dishevelled/dsh-bio-adam/1.0.1 [JAR] dsh-bio-adam-1.0.jar in org/dishevelled/dsh-bio-adam/1.0 [JAR] dsh-bio-compress-hdfs-2.2.jar in org/dishevelled/dsh-bio-compress-hdfs/2.2 [JAR] annotations-0.6.1.144.jar in org/forome/annotations/0.6.1.144 [JAR] astorage-1.0.0p13.jar in org/forome/astorage/1.0.0p13 [JAR] astorage.core-1.0.0p13.jar in org/forome/astorage.core/1.0.0p13 [JAR] astorage-1.0.0p13.jar in org/forome/astorage/astorage/1.0.0p13 [JAR] gweaver-bulk-import-1.7.11-jar-with-dependencies.jar in org/geneweaver/gweaver-bulk-import/1.7.11 [JAR] gweaver-query-engine-1.3.3-jar-with-deps-merge-services.jar in org/geneweaver/gweaver-query-engine/1.3.3 [JAR] gweaver-query-engine-1.2.0-jar-with-dependencies.jar in org/geneweaver/gweaver-query-engine/1.2.0 [JAR] gweaver-stream-io-2.9.8-jar-with-dependencies.jar in org/geneweaver/gweaver-stream-io/2.9.8 [JAR] genomicsdb-1.5.5-allinone.jar in org/genomicsdb/genomicsdb/1.5.5 [JAR] genomicsdb-1.1.0.1-jar-with-dependencies.jar in org/genomicsdb/genomicsdb/1.1.0.1 [JAR] cli_2.11-1.2.0-M1-assembly.jar in org/hammerlab/bam/cli_2.11/1.2.0-M1 [JAR] cli_2.11-1.1.0-assembly.jar in org/hammerlab/bam/cli_2.11/1.1.0 [JAR] cli_2.11-1.0.0-assembly.jar in org/hammerlab/bam/cli_2.11/1.0.0 [JAR] vitt-cli-0.1.0.jar in org/monarchinitiative/vitt/vitt-cli/0.1.0 [JAR] hpg-bigdata-app-0.6.0-jar-with-dependencies.jar in org/opencb/hpg-bigdata/hpg-bigdata-app/0.6.0 [JAR] opencga-storage-hadoop-core-2.12.9-jar-with-dependencies.jar in org/opencb/opencga/opencga-storage-hadoop-core/2.12.9 [JAR] opencga-storage-hadoop-lib-hdp3.1-4.0.0-jar-with-dependencies.jar in org/opencb/opencga/opencga-storage-hadoop-lib-hdp3.1/4.0.0 [JAR] oskar-spark-0.2.1-jar-with-dependencies.jar in org/opencb/oskar/oskar-spark/0.2.1