Files in mskilab/bambi
R to query barcode indices on bam files

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/R6_class.R R/RcppExports.R R/utils.R README.md
config.log
config.status
configure
configure.ac
man/bambi-package.Rd man/bambi.Rd man/check_index.Rd man/internal.Rd man/parse_outputs.Rd man/query_bam_index.Rd
src/Makevars
src/Makevars.in
src/RcppExports.cpp
src/bambi.cpp
src/bamdb/.gitignore
src/bamdb/.travis.yml
src/bamdb/.ycm_extra_conf.py
src/bamdb/CMakeLists.txt
src/bamdb/Dockerfile
src/bamdb/LICENSE
src/bamdb/Singularity.bamdb
src/bamdb/cmake/FindCK.cmake
src/bamdb/cmake/FindHTSlib.cmake
src/bamdb/cmake/FindLMDB.cmake
src/bamdb/cmake/LibFindMacros.cmake
src/bamdb/include/bam_api.h
src/bamdb/include/bamdb.h
src/bamdb/include/bamdb_index_writer.h
src/bamdb/include/bamdb_lmdb.h
src/bamdb/include/bamdb_status.h
src/bamdb/src/bam_api.c
src/bamdb/src/bamdb.c
src/bamdb/src/bamdb_index_writer.c
src/bamdb/src/bamdb_lmdb.c
src/bamdb/src/bamdb_main.c
src/ck/.drone.yml
src/ck/.gitignore
src/ck/.travis.yml
src/ck/LICENSE
src/ck/Makefile.in
src/ck/README.md
src/ck/build/ck.build.aarch64
src/ck/build/ck.build.arm
src/ck/build/ck.build.in
src/ck/build/ck.build.ppc
src/ck/build/ck.build.ppc64
src/ck/build/ck.build.s390x
src/ck/build/ck.build.sparcv9
src/ck/build/ck.build.x86
src/ck/build/ck.build.x86_64
src/ck/build/ck.pc.in
src/ck/build/ck.spec.in
src/ck/build/regressions.build.in
src/ck/configure
src/ck/doc/CK_ARRAY_FOREACH
src/ck/doc/CK_COHORT_INIT
src/ck/doc/CK_COHORT_INSTANCE
src/ck/doc/CK_COHORT_LOCK
src/ck/doc/CK_COHORT_PROTOTYPE
src/ck/doc/CK_COHORT_TRYLOCK
src/ck/doc/CK_COHORT_TRYLOCK_PROTOTYPE
src/ck/doc/CK_COHORT_UNLOCK
src/ck/doc/CK_HS_HASH
src/ck/doc/CK_RHS_HASH
src/ck/doc/CK_RWCOHORT_INIT
src/ck/doc/CK_RWCOHORT_INSTANCE
src/ck/doc/CK_RWCOHORT_PROTOTYPE
src/ck/doc/CK_RWCOHORT_READ_LOCK
src/ck/doc/CK_RWCOHORT_READ_UNLOCK
src/ck/doc/CK_RWCOHORT_WRITE_LOCK
src/ck/doc/CK_RWCOHORT_WRITE_UNLOCK
src/ck/doc/Makefile.in
src/ck/doc/ck_array_buffer
src/ck/doc/ck_array_commit
src/ck/doc/ck_array_deinit
src/ck/doc/ck_array_init
src/ck/doc/ck_array_initialized
src/ck/doc/ck_array_length
src/ck/doc/ck_array_put
src/ck/doc/ck_array_put_unique
src/ck/doc/ck_array_remove
src/ck/doc/ck_bitmap_base
src/ck/doc/ck_bitmap_bits
src/ck/doc/ck_bitmap_bts
src/ck/doc/ck_bitmap_buffer
src/ck/doc/ck_bitmap_clear
src/ck/doc/ck_bitmap_init
src/ck/doc/ck_bitmap_iterator_init
src/ck/doc/ck_bitmap_next
src/ck/doc/ck_bitmap_reset
src/ck/doc/ck_bitmap_set
src/ck/doc/ck_bitmap_size
src/ck/doc/ck_bitmap_test
src/ck/doc/ck_bitmap_union
src/ck/doc/ck_brlock
src/ck/doc/ck_cohort
src/ck/doc/ck_elide
src/ck/doc/ck_epoch_barrier
src/ck/doc/ck_epoch_begin
src/ck/doc/ck_epoch_call
src/ck/doc/ck_epoch_end
src/ck/doc/ck_epoch_init
src/ck/doc/ck_epoch_poll
src/ck/doc/ck_epoch_reclaim
src/ck/doc/ck_epoch_recycle
src/ck/doc/ck_epoch_register
src/ck/doc/ck_epoch_synchronize
src/ck/doc/ck_epoch_unregister
src/ck/doc/ck_hs_apply
src/ck/doc/ck_hs_count
src/ck/doc/ck_hs_destroy
src/ck/doc/ck_hs_fas
src/ck/doc/ck_hs_gc
src/ck/doc/ck_hs_get
src/ck/doc/ck_hs_grow
src/ck/doc/ck_hs_init
src/ck/doc/ck_hs_iterator_init
src/ck/doc/ck_hs_move
src/ck/doc/ck_hs_next
src/ck/doc/ck_hs_put
src/ck/doc/ck_hs_put_unique
src/ck/doc/ck_hs_rebuild
src/ck/doc/ck_hs_remove
src/ck/doc/ck_hs_reset
src/ck/doc/ck_hs_reset_size
src/ck/doc/ck_hs_set
src/ck/doc/ck_hs_stat
src/ck/doc/ck_ht_count
src/ck/doc/ck_ht_destroy
src/ck/doc/ck_ht_entry_empty
src/ck/doc/ck_ht_entry_key
src/ck/doc/ck_ht_entry_key_direct
src/ck/doc/ck_ht_entry_key_length
src/ck/doc/ck_ht_entry_key_set
src/ck/doc/ck_ht_entry_key_set_direct
src/ck/doc/ck_ht_entry_set
src/ck/doc/ck_ht_entry_set_direct
src/ck/doc/ck_ht_entry_value
src/ck/doc/ck_ht_entry_value_direct
src/ck/doc/ck_ht_gc
src/ck/doc/ck_ht_get_spmc
src/ck/doc/ck_ht_grow_spmc
src/ck/doc/ck_ht_hash
src/ck/doc/ck_ht_hash_direct
src/ck/doc/ck_ht_init
src/ck/doc/ck_ht_iterator_init
src/ck/doc/ck_ht_next
src/ck/doc/ck_ht_put_spmc
src/ck/doc/ck_ht_remove_spmc
src/ck/doc/ck_ht_reset_size_spmc
src/ck/doc/ck_ht_reset_spmc
src/ck/doc/ck_ht_set_spmc
src/ck/doc/ck_ht_stat
src/ck/doc/ck_pflock
src/ck/doc/ck_pr
src/ck/doc/ck_pr_add
src/ck/doc/ck_pr_and
src/ck/doc/ck_pr_barrier
src/ck/doc/ck_pr_btc
src/ck/doc/ck_pr_btr
src/ck/doc/ck_pr_bts
src/ck/doc/ck_pr_cas
src/ck/doc/ck_pr_dec
src/ck/doc/ck_pr_faa
src/ck/doc/ck_pr_fas
src/ck/doc/ck_pr_fence_acquire
src/ck/doc/ck_pr_fence_atomic
src/ck/doc/ck_pr_fence_atomic_load
src/ck/doc/ck_pr_fence_atomic_store
src/ck/doc/ck_pr_fence_load
src/ck/doc/ck_pr_fence_load_atomic
src/ck/doc/ck_pr_fence_load_depends
src/ck/doc/ck_pr_fence_load_store
src/ck/doc/ck_pr_fence_memory
src/ck/doc/ck_pr_fence_release
src/ck/doc/ck_pr_fence_store
src/ck/doc/ck_pr_fence_store_atomic
src/ck/doc/ck_pr_fence_store_load
src/ck/doc/ck_pr_inc
src/ck/doc/ck_pr_load
src/ck/doc/ck_pr_neg
src/ck/doc/ck_pr_not
src/ck/doc/ck_pr_or
src/ck/doc/ck_pr_rtm
src/ck/doc/ck_pr_stall
src/ck/doc/ck_pr_store
src/ck/doc/ck_pr_sub
src/ck/doc/ck_pr_xor
src/ck/doc/ck_queue
src/ck/doc/ck_rhs_apply
src/ck/doc/ck_rhs_count
src/ck/doc/ck_rhs_destroy
src/ck/doc/ck_rhs_fas
src/ck/doc/ck_rhs_gc
src/ck/doc/ck_rhs_get
src/ck/doc/ck_rhs_grow
src/ck/doc/ck_rhs_init
src/ck/doc/ck_rhs_iterator_init
src/ck/doc/ck_rhs_move
src/ck/doc/ck_rhs_next
src/ck/doc/ck_rhs_put
src/ck/doc/ck_rhs_put_unique
src/ck/doc/ck_rhs_rebuild
src/ck/doc/ck_rhs_remove
src/ck/doc/ck_rhs_reset
src/ck/doc/ck_rhs_reset_size
src/ck/doc/ck_rhs_set
src/ck/doc/ck_rhs_set_load_factor
src/ck/doc/ck_rhs_stat
src/ck/doc/ck_ring_capacity
src/ck/doc/ck_ring_dequeue_spmc
src/ck/doc/ck_ring_dequeue_spsc
src/ck/doc/ck_ring_enqueue_spmc
src/ck/doc/ck_ring_enqueue_spmc_size
src/ck/doc/ck_ring_enqueue_spsc
src/ck/doc/ck_ring_enqueue_spsc_size
src/ck/doc/ck_ring_init
src/ck/doc/ck_ring_size
src/ck/doc/ck_ring_trydequeue_spmc
src/ck/doc/ck_rwcohort
src/ck/doc/ck_rwlock
src/ck/doc/ck_sequence
src/ck/doc/ck_spinlock
src/ck/doc/ck_swlock
src/ck/doc/ck_tflock
src/ck/doc/refcheck.pl
src/ck/include/ck_array.h
src/ck/include/ck_backoff.h
src/ck/include/ck_barrier.h
src/ck/include/ck_bitmap.h
src/ck/include/ck_brlock.h
src/ck/include/ck_bytelock.h
src/ck/include/ck_cc.h
src/ck/include/ck_cohort.h
src/ck/include/ck_elide.h
src/ck/include/ck_epoch.h
src/ck/include/ck_fifo.h
src/ck/include/ck_hp.h
src/ck/include/ck_hp_fifo.h
src/ck/include/ck_hp_stack.h
src/ck/include/ck_hs.h
src/ck/include/ck_ht.h
src/ck/include/ck_limits.h
src/ck/include/ck_malloc.h
src/ck/include/ck_md.h.in
src/ck/include/ck_pflock.h
src/ck/include/ck_pr.h
src/ck/include/ck_queue.h
src/ck/include/ck_rhs.h
src/ck/include/ck_ring.h
src/ck/include/ck_rwcohort.h
src/ck/include/ck_rwlock.h
src/ck/include/ck_sequence.h
src/ck/include/ck_spinlock.h
src/ck/include/ck_stack.h
src/ck/include/ck_stdbool.h
src/ck/include/ck_stddef.h
src/ck/include/ck_stdint.h
src/ck/include/ck_stdlib.h
src/ck/include/ck_string.h
src/ck/include/ck_swlock.h
src/ck/include/ck_tflock.h
src/ck/include/freebsd/ck_md.h.in
src/ck/include/gcc/aarch64/ck_f_pr.h
src/ck/include/gcc/aarch64/ck_pr.h
src/ck/include/gcc/aarch64/ck_pr_llsc.h
src/ck/include/gcc/aarch64/ck_pr_lse.h
src/ck/include/gcc/arm/ck_f_pr.h
src/ck/include/gcc/arm/ck_pr.h
src/ck/include/gcc/ck_cc.h
src/ck/include/gcc/ck_f_pr.h
src/ck/include/gcc/ck_pr.h
src/ck/include/gcc/ppc/ck_f_pr.h
src/ck/include/gcc/ppc/ck_pr.h
src/ck/include/gcc/ppc64/ck_f_pr.h
src/ck/include/gcc/ppc64/ck_pr.h
src/ck/include/gcc/s390x/ck_f_pr.h
src/ck/include/gcc/s390x/ck_pr.h
src/ck/include/gcc/sparcv9/ck_f_pr.h
src/ck/include/gcc/sparcv9/ck_pr.h
src/ck/include/gcc/x86/ck_f_pr.h
src/ck/include/gcc/x86/ck_pr.h
src/ck/include/gcc/x86_64/ck_f_pr.h
src/ck/include/gcc/x86_64/ck_pr.h
src/ck/include/gcc/x86_64/ck_pr_rtm.h
src/ck/include/spinlock/anderson.h
src/ck/include/spinlock/cas.h
src/ck/include/spinlock/clh.h
src/ck/include/spinlock/dec.h
src/ck/include/spinlock/fas.h
src/ck/include/spinlock/hclh.h
src/ck/include/spinlock/mcs.h
src/ck/include/spinlock/ticket.h
src/ck/regressions/Makefile
src/ck/regressions/Makefile.unsupported
src/ck/regressions/ck_array/validate/Makefile
src/ck/regressions/ck_array/validate/serial.c
src/ck/regressions/ck_backoff/validate/Makefile
src/ck/regressions/ck_backoff/validate/validate.c
src/ck/regressions/ck_barrier/benchmark/Makefile
src/ck/regressions/ck_barrier/benchmark/throughput.c
src/ck/regressions/ck_barrier/validate/Makefile
src/ck/regressions/ck_barrier/validate/barrier_centralized.c
src/ck/regressions/ck_barrier/validate/barrier_combining.c
src/ck/regressions/ck_barrier/validate/barrier_dissemination.c
src/ck/regressions/ck_barrier/validate/barrier_mcs.c
src/ck/regressions/ck_barrier/validate/barrier_tournament.c
src/ck/regressions/ck_bitmap/validate/Makefile
src/ck/regressions/ck_bitmap/validate/serial.c
src/ck/regressions/ck_brlock/benchmark/Makefile
src/ck/regressions/ck_brlock/benchmark/latency.c
src/ck/regressions/ck_brlock/benchmark/throughput.c
src/ck/regressions/ck_brlock/validate/Makefile
src/ck/regressions/ck_brlock/validate/validate.c
src/ck/regressions/ck_bytelock/benchmark/Makefile
src/ck/regressions/ck_bytelock/benchmark/latency.c
src/ck/regressions/ck_bytelock/validate/Makefile
src/ck/regressions/ck_bytelock/validate/validate.c
src/ck/regressions/ck_cc/validate/Makefile
src/ck/regressions/ck_cc/validate/ck_cc.c
src/ck/regressions/ck_cohort/benchmark/Makefile
src/ck/regressions/ck_cohort/benchmark/ck_cohort.c
src/ck/regressions/ck_cohort/benchmark/throughput.c
src/ck/regressions/ck_cohort/ck_cohort.h
src/ck/regressions/ck_cohort/validate/Makefile
src/ck/regressions/ck_cohort/validate/validate.c
src/ck/regressions/ck_epoch/validate/Makefile
src/ck/regressions/ck_epoch/validate/ck_epoch_call.c
src/ck/regressions/ck_epoch/validate/ck_epoch_poll.c
src/ck/regressions/ck_epoch/validate/ck_epoch_section.c
src/ck/regressions/ck_epoch/validate/ck_epoch_section_2.c
src/ck/regressions/ck_epoch/validate/ck_epoch_synchronize.c
src/ck/regressions/ck_epoch/validate/ck_stack.c
src/ck/regressions/ck_epoch/validate/torture.c
src/ck/regressions/ck_fifo/benchmark/Makefile
src/ck/regressions/ck_fifo/benchmark/latency.c
src/ck/regressions/ck_fifo/validate/Makefile
src/ck/regressions/ck_fifo/validate/ck_fifo_mpmc.c
src/ck/regressions/ck_fifo/validate/ck_fifo_mpmc_iterator.c
src/ck/regressions/ck_fifo/validate/ck_fifo_spsc.c
src/ck/regressions/ck_fifo/validate/ck_fifo_spsc_iterator.c
src/ck/regressions/ck_hp/benchmark/Makefile
src/ck/regressions/ck_hp/benchmark/fifo_latency.c
src/ck/regressions/ck_hp/benchmark/stack_latency.c
src/ck/regressions/ck_hp/validate/Makefile
src/ck/regressions/ck_hp/validate/ck_hp_fifo.c
src/ck/regressions/ck_hp/validate/ck_hp_fifo_donner.c
src/ck/regressions/ck_hp/validate/ck_hp_stack.c
src/ck/regressions/ck_hp/validate/nbds_haz_test.c
src/ck/regressions/ck_hp/validate/serial.c
src/ck/regressions/ck_hs/benchmark/Makefile
src/ck/regressions/ck_hs/benchmark/apply.c
src/ck/regressions/ck_hs/benchmark/parallel_bytestring.c
src/ck/regressions/ck_hs/benchmark/serial.c
src/ck/regressions/ck_hs/validate/Makefile
src/ck/regressions/ck_hs/validate/serial.c
src/ck/regressions/ck_ht/benchmark/Makefile
src/ck/regressions/ck_ht/benchmark/parallel_bytestring.c
src/ck/regressions/ck_ht/benchmark/parallel_direct.c
src/ck/regressions/ck_ht/benchmark/serial.c
src/ck/regressions/ck_ht/validate/Makefile
src/ck/regressions/ck_ht/validate/serial.c
src/ck/regressions/ck_pflock/benchmark/Makefile
src/ck/regressions/ck_pflock/benchmark/latency.c
src/ck/regressions/ck_pflock/benchmark/throughput.c
src/ck/regressions/ck_pflock/validate/Makefile
src/ck/regressions/ck_pflock/validate/validate.c
src/ck/regressions/ck_pr/benchmark/Makefile
src/ck/regressions/ck_pr/benchmark/benchmark.h
src/ck/regressions/ck_pr/benchmark/ck_pr_add_64.c
src/ck/regressions/ck_pr/benchmark/ck_pr_cas_64.c
src/ck/regressions/ck_pr/benchmark/ck_pr_cas_64_2.c
src/ck/regressions/ck_pr/benchmark/ck_pr_faa_64.c
src/ck/regressions/ck_pr/benchmark/ck_pr_fas_64.c
src/ck/regressions/ck_pr/benchmark/ck_pr_neg_64.c
src/ck/regressions/ck_pr/benchmark/fp.c
src/ck/regressions/ck_pr/validate/Makefile
src/ck/regressions/ck_pr/validate/ck_pr_add.c
src/ck/regressions/ck_pr/validate/ck_pr_and.c
src/ck/regressions/ck_pr/validate/ck_pr_bin.c
src/ck/regressions/ck_pr/validate/ck_pr_btc.c
src/ck/regressions/ck_pr/validate/ck_pr_btr.c
src/ck/regressions/ck_pr/validate/ck_pr_bts.c
src/ck/regressions/ck_pr/validate/ck_pr_btx.c
src/ck/regressions/ck_pr/validate/ck_pr_cas.c
src/ck/regressions/ck_pr/validate/ck_pr_dec.c
src/ck/regressions/ck_pr/validate/ck_pr_dec_zero.c
src/ck/regressions/ck_pr/validate/ck_pr_faa.c
src/ck/regressions/ck_pr/validate/ck_pr_fas.c
src/ck/regressions/ck_pr/validate/ck_pr_fax.c
src/ck/regressions/ck_pr/validate/ck_pr_fence.c
src/ck/regressions/ck_pr/validate/ck_pr_inc.c
src/ck/regressions/ck_pr/validate/ck_pr_inc_zero.c
src/ck/regressions/ck_pr/validate/ck_pr_load.c
src/ck/regressions/ck_pr/validate/ck_pr_n.c
src/ck/regressions/ck_pr/validate/ck_pr_or.c
src/ck/regressions/ck_pr/validate/ck_pr_store.c
src/ck/regressions/ck_pr/validate/ck_pr_sub.c
src/ck/regressions/ck_pr/validate/ck_pr_unary.c
src/ck/regressions/ck_pr/validate/ck_pr_xor.c
src/ck/regressions/ck_queue/validate/Makefile
src/ck/regressions/ck_queue/validate/ck_list.c
src/ck/regressions/ck_queue/validate/ck_slist.c
src/ck/regressions/ck_queue/validate/ck_stailq.c
src/ck/regressions/ck_rhs/benchmark/Makefile
src/ck/regressions/ck_rhs/benchmark/parallel_bytestring.c
src/ck/regressions/ck_rhs/benchmark/serial.c
src/ck/regressions/ck_rhs/validate/Makefile
src/ck/regressions/ck_rhs/validate/serial.c
src/ck/regressions/ck_ring/benchmark/Makefile
src/ck/regressions/ck_ring/benchmark/latency.c
src/ck/regressions/ck_ring/validate/Makefile
src/ck/regressions/ck_ring/validate/ck_ring_mpmc.c
src/ck/regressions/ck_ring/validate/ck_ring_mpmc_template.c
src/ck/regressions/ck_ring/validate/ck_ring_spmc.c
src/ck/regressions/ck_ring/validate/ck_ring_spmc_template.c
src/ck/regressions/ck_ring/validate/ck_ring_spsc.c
src/ck/regressions/ck_rwcohort/benchmark/Makefile
src/ck/regressions/ck_rwcohort/benchmark/ck_neutral.c
src/ck/regressions/ck_rwcohort/benchmark/ck_rp.c
src/ck/regressions/ck_rwcohort/benchmark/ck_wp.c
src/ck/regressions/ck_rwcohort/benchmark/latency.h
src/ck/regressions/ck_rwcohort/benchmark/throughput.h
src/ck/regressions/ck_rwcohort/ck_neutral.h
src/ck/regressions/ck_rwcohort/ck_rp.h
src/ck/regressions/ck_rwcohort/ck_wp.h
src/ck/regressions/ck_rwcohort/validate/Makefile
src/ck/regressions/ck_rwcohort/validate/ck_neutral.c
src/ck/regressions/ck_rwcohort/validate/ck_rp.c
src/ck/regressions/ck_rwcohort/validate/ck_wp.c
src/ck/regressions/ck_rwcohort/validate/validate.h
src/ck/regressions/ck_rwlock/benchmark/Makefile
src/ck/regressions/ck_rwlock/benchmark/latency.c
src/ck/regressions/ck_rwlock/benchmark/throughput.c
src/ck/regressions/ck_rwlock/validate/Makefile
src/ck/regressions/ck_rwlock/validate/validate.c
src/ck/regressions/ck_sequence/benchmark/Makefile
src/ck/regressions/ck_sequence/benchmark/ck_sequence.c
src/ck/regressions/ck_sequence/validate/Makefile
src/ck/regressions/ck_sequence/validate/ck_sequence.c
src/ck/regressions/ck_spinlock/benchmark/Makefile
src/ck/regressions/ck_spinlock/benchmark/ck_anderson.c
src/ck/regressions/ck_spinlock/benchmark/ck_cas.c
src/ck/regressions/ck_spinlock/benchmark/ck_clh.c
src/ck/regressions/ck_spinlock/benchmark/ck_dec.c
src/ck/regressions/ck_spinlock/benchmark/ck_fas.c
src/ck/regressions/ck_spinlock/benchmark/ck_hclh.c
src/ck/regressions/ck_spinlock/benchmark/ck_mcs.c
src/ck/regressions/ck_spinlock/benchmark/ck_spinlock.c
src/ck/regressions/ck_spinlock/benchmark/ck_ticket.c
src/ck/regressions/ck_spinlock/benchmark/ck_ticket_pb.c
src/ck/regressions/ck_spinlock/benchmark/latency.h
src/ck/regressions/ck_spinlock/benchmark/linux_spinlock.c
src/ck/regressions/ck_spinlock/benchmark/throughput.h
src/ck/regressions/ck_spinlock/ck_anderson.h
src/ck/regressions/ck_spinlock/ck_cas.h
src/ck/regressions/ck_spinlock/ck_clh.h
src/ck/regressions/ck_spinlock/ck_dec.h
src/ck/regressions/ck_spinlock/ck_fas.h
src/ck/regressions/ck_spinlock/ck_hclh.h
src/ck/regressions/ck_spinlock/ck_mcs.h
src/ck/regressions/ck_spinlock/ck_spinlock.h
src/ck/regressions/ck_spinlock/ck_ticket.h
src/ck/regressions/ck_spinlock/ck_ticket_pb.h
src/ck/regressions/ck_spinlock/linux_spinlock.h
src/ck/regressions/ck_spinlock/validate/Makefile
src/ck/regressions/ck_spinlock/validate/ck_anderson.c
src/ck/regressions/ck_spinlock/validate/ck_cas.c
src/ck/regressions/ck_spinlock/validate/ck_clh.c
src/ck/regressions/ck_spinlock/validate/ck_dec.c
src/ck/regressions/ck_spinlock/validate/ck_fas.c
src/ck/regressions/ck_spinlock/validate/ck_hclh.c
src/ck/regressions/ck_spinlock/validate/ck_mcs.c
src/ck/regressions/ck_spinlock/validate/ck_spinlock.c
src/ck/regressions/ck_spinlock/validate/ck_ticket.c
src/ck/regressions/ck_spinlock/validate/ck_ticket_pb.c
src/ck/regressions/ck_spinlock/validate/linux_spinlock.c
src/ck/regressions/ck_spinlock/validate/validate.h
src/ck/regressions/ck_stack/benchmark/Makefile
src/ck/regressions/ck_stack/benchmark/latency.c
src/ck/regressions/ck_stack/validate/Makefile
src/ck/regressions/ck_stack/validate/pair.c
src/ck/regressions/ck_stack/validate/pop.c
src/ck/regressions/ck_stack/validate/push.c
src/ck/regressions/ck_stack/validate/serial.c
src/ck/regressions/ck_swlock/benchmark/Makefile
src/ck/regressions/ck_swlock/benchmark/latency.c
src/ck/regressions/ck_swlock/benchmark/throughput.c
src/ck/regressions/ck_swlock/validate/Makefile
src/ck/regressions/ck_swlock/validate/validate.c
src/ck/regressions/ck_tflock/benchmark/Makefile
src/ck/regressions/ck_tflock/benchmark/latency.c
src/ck/regressions/ck_tflock/benchmark/throughput.c
src/ck/regressions/ck_tflock/validate/Makefile
src/ck/regressions/ck_tflock/validate/validate.c
src/ck/regressions/common.h
src/ck/src/Makefile.in
src/ck/src/ck_array.c
src/ck/src/ck_barrier_centralized.c
src/ck/src/ck_barrier_combining.c
src/ck/src/ck_barrier_dissemination.c
src/ck/src/ck_barrier_mcs.c
src/ck/src/ck_barrier_tournament.c
src/ck/src/ck_epoch.c
src/ck/src/ck_hp.c
src/ck/src/ck_hs.c
src/ck/src/ck_ht.c
src/ck/src/ck_ht_hash.h
src/ck/src/ck_internal.h
src/ck/src/ck_rhs.c
src/ck/tools/ci-build.sh
src/ck/tools/feature.sh
src/htslib/.appveyor.yml
src/htslib/.gitattributes
src/htslib/.gitignore
src/htslib/.travis.yml
src/htslib/INSTALL
src/htslib/LICENSE
src/htslib/Makefile
src/htslib/NEWS
src/htslib/README
src/htslib/README.md
src/htslib/bcf_sr_sort.c
src/htslib/bcf_sr_sort.h
src/htslib/bgzf.c
src/htslib/bgzip.1
src/htslib/bgzip.c
src/htslib/config.mk.in
src/htslib/configure.ac
src/htslib/cram/cram.h
src/htslib/cram/cram_codecs.c
src/htslib/cram/cram_codecs.h
src/htslib/cram/cram_decode.c
src/htslib/cram/cram_decode.h
src/htslib/cram/cram_encode.c
src/htslib/cram/cram_encode.h
src/htslib/cram/cram_external.c
src/htslib/cram/cram_index.c
src/htslib/cram/cram_index.h
src/htslib/cram/cram_io.c
src/htslib/cram/cram_io.h
src/htslib/cram/cram_samtools.c
src/htslib/cram/cram_samtools.h
src/htslib/cram/cram_stats.c
src/htslib/cram/cram_stats.h
src/htslib/cram/cram_structs.h
src/htslib/cram/files.c
src/htslib/cram/mFILE.c
src/htslib/cram/mFILE.h
src/htslib/cram/misc.h
src/htslib/cram/open_trace_file.c
src/htslib/cram/open_trace_file.h
src/htslib/cram/os.h
src/htslib/cram/pooled_alloc.c
src/htslib/cram/pooled_alloc.h
src/htslib/cram/rANS_byte.h
src/htslib/cram/rANS_static.c
src/htslib/cram/rANS_static.h
src/htslib/cram/sam_header.c
src/htslib/cram/sam_header.h
src/htslib/cram/string_alloc.c
src/htslib/cram/string_alloc.h
src/htslib/errmod.c
src/htslib/faidx.5
src/htslib/faidx.c
src/htslib/hfile.c
src/htslib/hfile_gcs.c
src/htslib/hfile_internal.h
src/htslib/hfile_libcurl.c
src/htslib/hfile_net.c
src/htslib/hfile_s3.c
src/htslib/hts.c
src/htslib/hts_internal.h
src/htslib/hts_os.c
src/htslib/htsfile.1
src/htslib/htsfile.c
src/htslib/htslib.mk
src/htslib/htslib.pc.in
src/htslib/htslib/bgzf.h
src/htslib/htslib/cram.h
src/htslib/htslib/faidx.h
src/htslib/htslib/hfile.h
src/htslib/htslib/hts.h
src/htslib/htslib/hts_defs.h
src/htslib/htslib/hts_endian.h
src/htslib/htslib/hts_log.h
src/htslib/htslib/hts_os.h
src/htslib/htslib/kbitset.h
src/htslib/htslib/kfunc.h
src/htslib/htslib/khash.h
src/htslib/htslib/khash_str2int.h
src/htslib/htslib/klist.h
src/htslib/htslib/knetfile.h
src/htslib/htslib/kseq.h
src/htslib/htslib/ksort.h
src/htslib/htslib/kstring.h
src/htslib/htslib/regidx.h
src/htslib/htslib/sam.h
src/htslib/htslib/synced_bcf_reader.h
src/htslib/htslib/tbx.h
src/htslib/htslib/thread_pool.h
src/htslib/htslib/vcf.h
src/htslib/htslib/vcf_sweep.h
src/htslib/htslib/vcfutils.h
src/htslib/htslib_vars.mk
src/htslib/kfunc.c
src/htslib/knetfile.c
src/htslib/kstring.c
src/htslib/m4/hts_prog_cc_warnings.m4
src/htslib/md5.c
src/htslib/multipart.c
src/htslib/os/lzma_stub.h
src/htslib/os/rand.c
src/htslib/plugin.c
src/htslib/probaln.c
src/htslib/realn.c
src/htslib/regidx.c
src/htslib/sam.5
src/htslib/sam.c
src/htslib/synced_bcf_reader.c
src/htslib/tabix.1
src/htslib/tabix.c
src/htslib/tbx.c
src/htslib/test/auxf#values.sam
src/htslib/test/auxf#values_java.cram
src/htslib/test/auxf.fa
src/htslib/test/auxf.fa.fai
src/htslib/test/bgziptest.txt
src/htslib/test/bgziptest.txt.gz
src/htslib/test/bgziptest.txt.gz.gzi
src/htslib/test/c1#bounds.sam
src/htslib/test/c1#clip.sam
src/htslib/test/c1#noseq.sam
src/htslib/test/c1#pad1.sam
src/htslib/test/c1#pad2.sam
src/htslib/test/c1#pad3.sam
src/htslib/test/c1#unknown.sam
src/htslib/test/c1.fa
src/htslib/test/c1.fa.fai
src/htslib/test/c2#pad.sam
src/htslib/test/c2.fa
src/htslib/test/c2.fa.fai
src/htslib/test/ce#1.sam
src/htslib/test/ce#1000.sam
src/htslib/test/ce#2.sam
src/htslib/test/ce#5.sam
src/htslib/test/ce#5b.sam
src/htslib/test/ce#5b_java.cram
src/htslib/test/ce#large_seq.sam
src/htslib/test/ce#supp.sam
src/htslib/test/ce#tag_depadded.sam
src/htslib/test/ce#tag_padded.sam
src/htslib/test/ce#unmap.sam
src/htslib/test/ce#unmap1.sam
src/htslib/test/ce#unmap2.sam
src/htslib/test/ce.fa
src/htslib/test/ce.fa.fai
src/htslib/test/compare_sam.pl
src/htslib/test/cross_validate.sh
src/htslib/test/faidx.fa
src/htslib/test/fieldarith.c
src/htslib/test/fieldarith.sam
src/htslib/test/formatcols.vcf
src/htslib/test/formatmissing-out.vcf
src/htslib/test/formatmissing.vcf
src/htslib/test/hfile.c
src/htslib/test/hts_endian.c
src/htslib/test/md#1.sam
src/htslib/test/md.fa
src/htslib/test/md.fa.fai
src/htslib/test/noroundtrip-out.vcf
src/htslib/test/noroundtrip.vcf
src/htslib/test/range.bam
src/htslib/test/range.bam.bai
src/htslib/test/range.cram
src/htslib/test/range.cram.crai
src/htslib/test/range.out
src/htslib/test/realn01.fa
src/htslib/test/realn01.fa.fai
src/htslib/test/realn01.sam
src/htslib/test/realn01_exp-a.sam
src/htslib/test/realn01_exp-e.sam
src/htslib/test/realn01_exp.sam
src/htslib/test/realn02-r.sam
src/htslib/test/realn02.fa
src/htslib/test/realn02.fa.fai
src/htslib/test/realn02.sam
src/htslib/test/realn02_exp-a.sam
src/htslib/test/realn02_exp-e.sam
src/htslib/test/realn02_exp.sam
src/htslib/test/sam.c
src/htslib/test/tabix/bed_file.Y.100200.out
src/htslib/test/tabix/bed_file.bed
src/htslib/test/tabix/gff_file.X.2934832.2935190.out
src/htslib/test/tabix/gff_file.gff
src/htslib/test/tabix/large_chr.20.1.2147483647.out
src/htslib/test/tabix/large_chr.vcf
src/htslib/test/tabix/tabix.tst
src/htslib/test/tabix/test-tabix.sh
src/htslib/test/tabix/vcf_file.1.3000151.out
src/htslib/test/tabix/vcf_file.2.3199812.out
src/htslib/test/tabix/vcf_file.vcf
src/htslib/test/test-bcf-sr.c
src/htslib/test/test-bcf-sr.pl
src/htslib/test/test-bcf-translate.c
src/htslib/test/test-bcf-translate.out
src/htslib/test/test-logging.pl
src/htslib/test/test-regidx.c
src/htslib/test/test-vcf-api.c
src/htslib/test/test-vcf-api.out
src/htslib/test/test-vcf-hdr-in.vcf
src/htslib/test/test-vcf-hdr.out
src/htslib/test/test-vcf-sweep.c
src/htslib/test/test-vcf-sweep.out
src/htslib/test/test.pl
src/htslib/test/test_bgzf.c
src/htslib/test/test_realn.c
src/htslib/test/test_view.c
src/htslib/test/thrash_threads1.c
src/htslib/test/thrash_threads2.c
src/htslib/test/thrash_threads3.c
src/htslib/test/thrash_threads4.c
src/htslib/test/thrash_threads5.c
src/htslib/test/thrash_threads6.c
src/htslib/test/thread_pool.md
src/htslib/test/xx#blank.sam
src/htslib/test/xx#large_aux.sam
src/htslib/test/xx#large_aux2.sam
src/htslib/test/xx#large_aux_java.cram
src/htslib/test/xx#minimal.sam
src/htslib/test/xx#pair.sam
src/htslib/test/xx#repeated.sam
src/htslib/test/xx#rg.sam
src/htslib/test/xx#tlen.sam
src/htslib/test/xx#tlen2.sam
src/htslib/test/xx#triplet.sam
src/htslib/test/xx#unsorted.sam
src/htslib/test/xx.fa
src/htslib/test/xx.fa.fai
src/htslib/textutils.c
src/htslib/textutils_internal.h
src/htslib/thread_pool.c
src/htslib/thread_pool_internal.h
src/htslib/vcf.5
src/htslib/vcf.c
src/htslib/vcf_sweep.c
src/htslib/vcfutils.c
src/htslib/version.sh
src/lmdb/libraries/liblmdb/.gitignore
src/lmdb/libraries/liblmdb/COPYRIGHT
src/lmdb/libraries/liblmdb/Doxyfile
src/lmdb/libraries/liblmdb/LICENSE
src/lmdb/libraries/liblmdb/Makefile
src/lmdb/libraries/liblmdb/intro.doc
src/lmdb/libraries/liblmdb/lmdb.h
src/lmdb/libraries/liblmdb/mdb.c
src/lmdb/libraries/liblmdb/mdb_copy.1
src/lmdb/libraries/liblmdb/mdb_copy.c
src/lmdb/libraries/liblmdb/mdb_drop.1
src/lmdb/libraries/liblmdb/mdb_drop.c
src/lmdb/libraries/liblmdb/mdb_dump.1
src/lmdb/libraries/liblmdb/mdb_dump.c
src/lmdb/libraries/liblmdb/mdb_load.1
src/lmdb/libraries/liblmdb/mdb_load.c
src/lmdb/libraries/liblmdb/mdb_stat.1
src/lmdb/libraries/liblmdb/mdb_stat.c
src/lmdb/libraries/liblmdb/midl.c
src/lmdb/libraries/liblmdb/midl.h
src/lmdb/libraries/liblmdb/mtest.c
src/lmdb/libraries/liblmdb/mtest2.c
src/lmdb/libraries/liblmdb/mtest3.c
src/lmdb/libraries/liblmdb/mtest4.c
src/lmdb/libraries/liblmdb/mtest5.c
src/lmdb/libraries/liblmdb/mtest6.c
src/lmdb/libraries/liblmdb/sample-bdb.txt
src/lmdb/libraries/liblmdb/sample-mdb.txt
src/lmdb/libraries/liblmdb/tooltag
src/symbols.rds
tests/testthat.R
tests/testthat/bam_with_no_lmdb.bam
tests/testthat/fake_bam.txt
tests/testthat/subset_HCC1143_phased_possorted000005.EnsemblStyle.PS.bam
tests/testthat/subset_HCC1143_phased_possorted000005.EnsemblStyle.PS.bam.bai
tests/testthat/subset_HCC1143_phased_possorted000005.EnsemblStyle.PS_lmdb/PS/data.mdb
tests/testthat/subset_HCC1143_phased_possorted000005.EnsemblStyle.PS_lmdb/QNAME/data.mdb
tests/testthat/subset_HCC1143_phased_possorted000005.EnsemblStyle.bam
tests/testthat/subset_HCC1143_phased_possorted000005.EnsemblStyle.bam.bai
tests/testthat/subset_HCC1143_phased_possorted000005.EnsemblStyle_lmdb/BX/data.mdb
tests/testthat/subset_HCC1143_phased_possorted000005.EnsemblStyle_lmdb/QNAME/data.mdb
tests/testthat/subset_HCC1143_phased_possorted000005.PS.bam
tests/testthat/subset_HCC1143_phased_possorted000005.PS.bam.bai
tests/testthat/subset_HCC1143_phased_possorted000005.PS_lmdb/PS/data.mdb
tests/testthat/subset_HCC1143_phased_possorted000005.PS_lmdb/QNAME/data.mdb
tests/testthat/subset_HCC1143_phased_possorted000005.bam
tests/testthat/subset_HCC1143_phased_possorted000005.bam.bai
tests/testthat/subset_HCC1143_phased_possorted000005_lmdb/BX/data.mdb
tests/testthat/subset_HCC1143_phased_possorted000005_lmdb/QNAME/data.mdb
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.CB.bam
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.CB.bam.bai
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.CB_lmdb/CB/data.mdb
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.CB_lmdb/QNAME/data.mdb
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UB.bam
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UB.bam.bai
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UB_lmdb/QNAME/data.mdb
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UB_lmdb/UB/data.mdb
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.CB.bam
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.CB.bam.bai
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.CB_lmdb/CB/data.mdb
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.CB_lmdb/QNAME/data.mdb
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.UB.bam
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.UB.bam.bai
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.UB_lmdb/QNAME/data.mdb
tests/testthat/subset_pbmc8k_possorted_genome_bam000025.UCSCstyle.UB_lmdb/UB/data.mdb
tests/testthat/test_bambi_ops.R
mskilab/bambi documentation built on May 14, 2019, 4:04 a.m.