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1 Noteworthy changes in release 1.2.1 (3 February 2015)
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2
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3 * Reinstated hts_file_type() and FT_* macros, which were available until 1.1
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4 but briefly removed in 1.2. This function is deprecated and will be removed
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5 in a future release -- you should use hts_detect_format() etc instead
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6
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7
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8 Noteworthy changes in release 1.2 (2 February 2015)
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9
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10 * HTSlib now has a configure script which checks your build environment
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11 and allows for selection of optional extras. See INSTALL for details
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12
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13 * By default, reference sequences are fetched from the EBI CRAM Reference
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14 Registry and cached in your $HOME cache directory. This behaviour can
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15 be controlled by setting REF_PATH and REF_CACHE enviroment variables
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16 (see the samtools(1) man page for details)
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17
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18 * Numerous CRAM improvements:
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19 - Support for CRAM v3.0, an upcoming revision to CRAM supporting
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20 better compression and per-container checksums
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21 - EOF checking for v2.1 and v3.0 (similar to checking BAM EOF blocks)
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22 - Non-standard values for PNEXT and TLEN fields are now preserved
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23 - hts_set_fai_filename() now provides a reference file when encoding
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24 - Generated read names are now numbered from 1, rather than being
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25 labelled 'slice:record-in-slice'
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26 - Multi-threading and speed improvements
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27
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28 * New htsfile command for identifying file formats, and corresponding
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29 file format detection APIs
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30
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31 * New tabix --regions FILE, --targets FILE options for filtering via BED files
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32
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33 * Optional iRODS file access, disabled by default. Configure with --with-irods
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34 to enable accessing iRODS data objects directly via 'irods:DATAOBJ'
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35
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36 * All occurences of 2^29 in the source have been eliminated, so indexing
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37 and querying against reference sequences larger than 512Mbp works (when
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38 using CSI indices)
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39
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40 * Support for plain GZIP compression in various places
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41
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42 * VCF header editing speed improvements
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43
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44 * Added seq_nt16_int[] (equivalent to the samtools API's bam_nt16_nt4_table)
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45
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46 * Reinstated faidx_fetch_nseq(), which was accidentally removed from 1.1.
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47 Now faidx_fetch_nseq() and faidx_nseq() are equivalent; eventually
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48 faidx_fetch_nseq() will be deprecated and removed [#156]
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49
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50 * Fixed bugs #141, #152, #155, #158, #159, and various memory leaks
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