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Count every inserted base in CRAM NM, and store bases past the reference end as htslib does Build and Test #747: Pull request #1850 synchronize by tfenne
8m 24s tf_cram_md_nm_parity
tf_cram_md_nm_parity
8m 24s
Count every inserted base in CRAM NM, and store bases past the reference end as htslib does Build and Test #746: Pull request #1850 opened by tfenne
9m 51s tf_cram_md_nm_parity
tf_cram_md_nm_parity
9m 51s
Read missing values, write negative doubles, report an empty VCF, and leave lazy genotypes undecoded by toString Build and Test #745: Pull request #1849 opened by tfenne
8m 4s tf_vcf_record_fixes
tf_vcf_record_fixes
8m 4s
Index FASTAs with blank lines as samtools does, read sequences past 2^30 bases, and don't treat plain gzip as indexable Build and Test #744: Pull request #1848 opened by tfenne
8m 28s tf_fasta_robustness
tf_fasta_robustness
8m 28s
Port the orphaned Scala tests to TestNG and list all three licences in the POM Build and Test #743: Pull request #1847 opened by tfenne
8m 28s tf_build_test_hygiene
tf_build_test_hygiene
8m 28s
Refuse unsorted records when indexing on the fly, and make closing twice harmless Build and Test #742: Pull request #1845 synchronize by tfenne
8m 24s tf_vcf_writer_order_close
tf_vcf_writer_order_close
8m 24s
Keep repeated VCF header lines and carry contig md5, URL and species Build and Test #741: Pull request #1846 opened by tfenne
7m 0s tf_vcf_header_fidelity
tf_vcf_header_fidelity
7m 0s
Refuse unsorted records when indexing on the fly, and make closing twice harmless Build and Test #740: Pull request #1845 opened by tfenne
5m 51s tf_vcf_writer_order_close
tf_vcf_writer_order_close
5m 51s
Build makeDefault() factories from current defaults, and sort-check records before the caller sees them Build and Test #739: Pull request #1844 opened by tfenne
6m 8s tf_samreader_factory_fixes
tf_samreader_factory_fixes
6m 8s
Keep unsigned B arrays through CRAM, and derive and store mate templa… Build and Test #738: Commit 10c16c3 pushed by tfenne
8m 36s master
master
8m 36s
Keep unsigned B arrays through CRAM, and derive and store mate template lengths as htslib does Build and Test #737: Pull request #1843 opened by tfenne
8m 53s tf_cram_unsigned_arrays_chain_tlen
tf_cram_unsigned_arrays_chain_tlen
8m 53s
Make indexed FASTA lookups safe to run concurrently, and write a .gzi… Build and Test #736: Commit 57f3b14 pushed by tfenne
8m 53s master
master
8m 53s
Make indexed FASTA lookups safe to run concurrently, and write a .gzi htsjdk can read Build and Test #735: Pull request #1842 synchronize by tfenne
7m 29s tf_indexed_fasta_concurrency
tf_indexed_fasta_concurrency
7m 29s
Make indexed FASTA lookups safe to run concurrently, and write a .gzi htsjdk can read Build and Test #734: Pull request #1842 opened by tfenne
8m 34s tf_indexed_fasta_concurrency
tf_indexed_fasta_concurrency
8m 34s
Write CG as B:I, encode SAM/BAM/CRAM text as the spec describes, and … Build and Test #733: Commit 442a10a pushed by tfenne
8m 22s master
master
8m 22s
Write CG as B:I, encode SAM/BAM/CRAM text as the spec describes, and refuse text that would corrupt it Build and Test #732: Pull request #1840 synchronize by tfenne
7m 50s tf_valid_sam_bam_output
tf_valid_sam_bam_output
7m 50s
Write CG as B:I, encode SAM/BAM/CRAM text as the spec describes, and refuse text that would corrupt it Build and Test #731: Pull request #1840 synchronize by tfenne
8m 38s tf_valid_sam_bam_output
tf_valid_sam_bam_output
8m 38s
Ask VCFHeaderVersion and BCFVersion what a version implies, not its n… Build and Test #730: Commit b2e88ef pushed by tfenne
8m 51s master
master
8m 51s
Ask VCFHeaderVersion and BCFVersion what a version implies, not its number Build and Test #729: Pull request #1841 opened by tfenne
8m 23s tf_vcf_version_methods
tf_vcf_version_methods
8m 23s
Parse breakend notation into a Breakend with its mate, strand and ins… Build and Test #728: Commit d13a4d2 pushed by tfenne
8m 12s master
master
8m 12s
Parse breakend notation into a Breakend with its mate, strand and inserted bases Build and Test #727: Pull request #1839 synchronize by tfenne
8m 44s tf_vcf_breakend
tf_vcf_breakend
8m 44s
Write CG as B:I, encode SAM/BAM/CRAM text as the spec describes, and refuse text that would corrupt it Build and Test #726: Pull request #1840 opened by tfenne
7m 6s tf_valid_sam_bam_output
tf_valid_sam_bam_output
7m 6s
Parse breakend notation into a Breakend with its mate, strand and inserted bases Build and Test #725: Pull request #1839 opened by tfenne
8m 27s tf_vcf_breakend
tf_vcf_breakend
8m 27s
Write real CRAM 3.0 again: a NORMAL_3_0 profile, codec checks by vers… Build and Test #724: Commit 795648b pushed by tfenne
12m 30s master
master
12m 30s
Write real CRAM 3.0 again: a NORMAL_3_0 profile, codec checks by version, and empty blocks htsjdk 4.x can read Build and Test #723: Pull request #1838 synchronize by tfenne
9m 7s tf_cram_30_codecs
tf_cram_30_codecs
9m 7s