Not applied to the first few tens of bases of each chromosome, leading Regardless of which -l or -r options are used (previously with -l it was * The mpileup command now applies BAQ calculations at all base positions, INFO/ADF, INFO/ADR -output-tags annotations that largely supersede Rather than X or as previously, and now has AD, ADF, ADR, INFO/AD, * The mpileup command now outputs the unseen allele in VCF/BCF as On the command line for compatibility with existing scripts). * The "bamshuf" command has been renamed to "collate" (hence the termīamshuf no longer appears in the documentation, though it still works ( samtools#295, samtools#349, samtools#356, samtools#418, PR samtools#441 see alsoĭiscussions in samtools#171, samtools#213.) If you are still using -f, -o, or out.prefix, convert to use -T PREFIXĪnd/or -o FILE instead. * The obsolete "samtools sort in.bam out.prefix" usage has been removed. Samtools release 1.3: many improvements, fixes, new commands (maybe you meant: _hts_getline, _bgzf_getline )Ĭollect2: error: ld returned 1 exit status Gcc -pthread -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o. Gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. If ( (getline(&res, &len, check) = -1 ) & Test/merge/test_bam_translate.c:386:5: warning: implicit declaration of function 'getline' Test/merge/test_bam_translate.c: In function 'main': I./htslib -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c I./htslib -c -o misc/wgsim.o misc/wgsim.c This is because the reverse read is frequently of lower quality that forward read and this information can be useful for tuning quality thresholds.Gcc -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. Also note that the summary for paired end data treats forward and reverse orientations of discord as separate categories. | ('unresolved', 'secondary_specific') | 265 | | ('unresolved', 'secondary_multi') | 46 | | ('unresolved', 'primary_specific') | 470 | | ('secondary_specific', 'unresolved') | 113 | | ('secondary_specific', 'unassigned') | 1230 | | ('secondary_specific', 'secondary_specific') | 995 | | ('secondary_specific', 'secondary_multi') | 333 | | ('secondary_specific', 'primary_specific') | 1597 | | ('secondary_specific', 'primary_multi') | 970 | | ('secondary_multi', 'unresolved') | 35 | | ('secondary_multi', 'secondary_specific') | 277 | | ('secondary_multi', 'secondary_multi') | 182 | | ('secondary_multi', 'primary_specific') | 523 | | ('primary_specific', 'unresolved') | 226 | | ('primary_specific', 'secondary_specific') | 1212 | | ('primary_specific', 'secondary_multi') | 554 | | ('primary_multi', 'secondary_specific') | 549 | Tools for using data from INSDC Sequence Read Archive Homebrew/science/sratoolkit: stable 2.5.4 (bottled), HEAD Skip use of libcurses, for platforms without it, or different curses naming Tools (written in C using htslib) for manipulating next-generation sequencing data Homebrew/science/samtools: stable 1.3 (bottled), HEAD usr/local/Cellar/bowtie2/2.2.6 (76 files, 20.4M) *īuild without using Intel Thread Building Blocks (TBB) Homebrew/science/bowtie2: stable 2.2.6 (bottled), HEAD
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