![]() We recommend recoding against the htslib API directly, but this addition * Added legacy API sam.h functions sam_index_load() and samfetch() providingīam_fetch()-style iteration over either BAM or CRAM files. * Samtools stats -target-regions option works again. (as used by Picard) from a FASTA reference file. * New samtools dict command, which creates a sequence dictionary * Added -a option to samtools depth to show all locations, including * Samtools stats now outputs separate "N" and "other" columns in theĪCGT content per cycle section ( samtools#376). * Samtools depad command now handles CIGAR N operators and acceptsĬRAM files ( samtools#201, samtools#404). * The tview command's colour scheme has been altered to be more suitableįor users with colour blindness ( samtools#457). (The versions named without "_core" are unchanged.) Or bam_prob_realn_core() functions, note that these now take an additional * If you have source code using bam_md.c's bam_fillmd1_core(), bam_cap_mapQ(), * Fixed calmd, targetcut, and potential mpileup segfaults when given brokenĪlignments with POS far beyond the end of their reference sequences. * Samtools index's optional index output path argument works again ( samtools#199). * Merging files with millions of headers now completes in a reasonableĪmount of time ( samtools#337, samtools#373, samtools#419, samtools#453 thanks to Nathan Weeks,Ĭhris Smowton, Martin Pollard, Rob Davies). Not recommended for most use ( samtools#159, samtools#252, samtools#291, samtools#393). * The rmdup command no longer immediately aborts (previously it alwaysĪborted with "bam_get_library() not yet implemented"), but remains * A new addreplacerg command that adds or alters headers and RG:Z That, you should now override LIBS rather than LDLIBS. Previously it listened to $(LDLIBS) instead if you were overriding * Samtools's Makefile now fully supports the standard convention ofĪllowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden as needed. * Samtools now has a configure script which checks your build environmentĪnd facilitates choosing which HTSlib to build against. ![]() 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 ![]()
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