[med-svn] samtools branch develop updated (85f1c53 -> eeb4b22)
Charles Plessy
plessy at moszumanska.debian.org
Thu Aug 21 22:58:53 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch develop
in repository samtools.
from 85f1c53 stats: realloc buffers in MPC calculation if necessary, unclipped length can be bigger seq_len
adds 63336cc Don't set text-is-cached flag if reading headers encountered EOF
adds 5fe45f3 Raise error if give @HD SO:coordinate to 'samtools fixmate'
adds fcdecf1 Merge pull request #20, fixmate aborts on SO:coordinate
adds bd5f0a0 Fix buffer overflow
adds 0bea4a7 Remove double fclose()
adds b53e632 Silence -Wstrict-prototypes warnings in main header files
adds 431a5e9 Catch overflow in n_cigar and give an explicit error.
adds bacb46c Merge cigar length check (PR #39)
adds 037bdb1 Fix control of compression level in bam_merge_core2
adds 63a54ff Set Git attributes similarly to the develop branch
adds 48b4b70 Release 0.1.20: final non-htslib standalone samtools
adds 69f08ea mpileup: Removed bcf_hdr_fmt_text() which is no longer necessary
adds 2bd2417 Implement view & bam2fq directly against the htslib API
adds dd48869 Updated test
adds 63f8590 flags: Fixed a typo
adds 839a16d mpileup: -q now takes effect also with -C
adds 66797d8 mpileup: Apply -Q switch also to MQ output
adds aa410be samtools flags: add documentation. print out decimal representation in addition to hexadecimal and string representation
adds 1b408f7 Merge pull request #121 from sm15/feature/bam_flags_docs
adds 660da5b Use new sam_itr_*() htslib API for BAM/CRAM iterators
adds e2d7559 [bedcov] Use the htslib API directly, now works with BAM or CRAM files
adds cbff696 Use htslib's bam_endpos() instead of copied old bam_calend() code
adds ce958a2 Fix typos in the manpage.
adds 4c09100 Merge pull request #118, fixing man page typos
adds f2abc5e fixed spelling mistake
adds 4f8660e Merge pull request #141 from sb10/develop
adds ce1efc6 Replace bam2fq numbers with existing constants
adds 66507a7 Remove global variables from samtools view
adds 296d029 Add ability to strip aux tags to samtools view
adds f3a306f Merge pull request #109 from aux_tag_strip of github.com/mp15/samtools
adds 41bcf93 Add properly paired to stats and correct definition in flagstat
adds dc6df77 Merge pull request #106, properly-paired flag statistics
adds c82cbad Shut up, clang!
adds df763f3 mpileup: Fixed broken IMF annotation
adds 55bb89e Added mpileup tests for CRAM
adds c643abc Make int size explicit for bcf_get_*_int calls
adds d85db72 Add some more comments to tview
adds b3376c4 Reenable tview and port to htslib
adds 917c3e1 Restore sample selection to tview and add a unit test for the code doing it.
adds 0b5be10 Use htslib facilities instead of bam_parse_region()
adds 54eaa39 Revert unnecessary changes on tview branch
adds a985c51 Fix tview-related dependencies
adds dd030b2 Merge pull request #93, convert tview to htslib API
adds 088b9d2 Use sam_itr_*()/etc, enabling tview on CRAM files
adds a8398f9 Fix "Usage: ..." message
adds 93dbf71 Added links to 'sister' projects.
adds 058b94f Merge #148, links to 'sister' projects (but omitting ourself)
adds 26bb0c4 stats: More understandable output fields naming
adds e3328b4 Updated mpileup test to reflect change in overlap quals
adds cbcbe48 Add a few comments to bam merging function
adds 29dcd07 WIP on header merging
adds 94eaa16 Add target id translation code and write pseudo code for building RG and PG translation tables
adds 6e03078 Convert PG and RG pseudo code to working code. Add pseudocode for PG PP: translation. Add -D_GNU_SOURCE for some of the newer POSIX functions
adds 3b2b9a5 Further work on bam merge to fix header produced
adds 2033785 Fix bugs picked up by unit testing. Make trans_tbl_t a named struct and move aside variable names the same as it.
adds 796fc4a More work on merging @RG and @PG tags into header.
adds 933445d Unit tests for merge
adds 9dfc2df add skeleton code for PP processing
adds 2ab1f3d NULLify some freed pointers. Add tracing statement
adds 6ea18e8 Unit test trans_tbl_init add test 5 for PG tags
adds 1a50bcc Fix memory leaks and finalise @PG PP handling
adds b3c4002 Test @PG merging and PP handling
adds 71ec46e Integrate new header merging code into bam_sort main function
adds dc65fbe Clean up old dead code
adds 7fdda46 Fix case where PG or RG tag is present on read but not in header. Fix translation of tid == -1 aka unmapped. Sort out extra \n in header text.
adds 63f7a33 Add test bams
adds 97797cc Fix spaces to tabs
adds c007fa0 Eliminate compiler warnings in a cross-platform safe way. Tweak comments a bit.
adds 3ff2373 Add unit test for bam_translate (WIP)
adds 988d565 Fix edge case
adds bcc1d24 Add unit test for tid translation
adds 7548729 Add additional unit tests for bam_translate for PG and RG tags.
adds 64cb9fd Adjust how merge handles duplicated PG and RG tags.
adds 6f494ec Add command line support for combining tags
adds c2667f5 Don't merge header into itself
adds b4f86f6 Correct header length in test
adds c5c128f Fix memory leak in trans_tbl_init Comment on MERGE_force
adds b73ff8e Enhance description of what we do
adds 563fcb6 Add warning when merging causes coordinate sort to be lost
adds 6abb25b Reorder merge code so that BAM gets translated before it is inserted into heap. Create reverse translation table for merge region selection. Define memset_pattern4 for non-OS X systems.
adds dde3359 Create slightly more sophisticated unit tests for merge
adds 38c6408 Convert merge reverse translation build to own function.
adds a936181 Ensure make only runs on make test Trap stderr in unit bam_translate test. Restructure bam_translate unit test for new format.
adds 06c849d Add clock based randomness to merge and option to fix random seed.
adds e4af837 Correct lost sort order detection in merge
adds 1f910e5 Fix regex to pick out sequence ids
adds edeacbb Add rtrans_build unit test stub
adds c8c818f More work on rtrans_build unit test. Update test makefile to include rtrans_build test. Add additional sam test file for merge to exercise missing target @SQ, especially in region merge.
adds 7a31715 Fix position of bam_translate in merge read loop.
adds 702b1f6 Deal with case where merged region does not exist in header of one of our input files. Update merge to htslib indexes.
adds 20f2b62 hts_iter_t is not a pointer unlike it's predecessor
adds f0e05f4 Add function to prettify header output by sorting it by defined order.
adds 85ee78d Instead of relying on NULL iter in merge use HTS_IDX_START
adds 45965ae Ignore generated test files Add additional test sam to test case where targets differ
adds 44b63f1 In bam sort and merge change: * pointer == 0 to == NULL * pointer = 0 to = NULL
adds 7c77832 Fix merge unit tests under Linux
adds a202dbe Initialise un-inited variable in test_bam_translate.
adds 1ffd06d Revise merge header matching regex from spec
adds 159f0cb Make it easier to tell merge test phases apart
adds a18dde7 Apparently some programs put spaces into their @PG and @RG ID's.
adds cf43d54 Add option to vary level of verbosity. Truncate file between tests. Correct test 6 for bam_translate.
adds d4d4867 Fix bug where wrong flag was being checked in header merge (merge rg vs merge pg) Add @RG PG tag rewriting, this all needs cleaning up and consolidating now.
adds 4c4da26 Add PG tags to @RG lines testcases.
adds 4e9bcf9 When merging instead of segfaulting when there is no index, return an error. Need to think of better ways to handle this.
adds 3dff60d Fix to use htslib commands.
adds e6ed9ca Port bam_sort.c completely to new API.
adds 275283a Fix up tests for htslib architecture
adds 46ca8f1 Add -b option to merge to allow the specification of a list of files as alternative to putting them on the command line.
adds 3ef90e9 Fix control of compression level in bam_merge_core. The setting was ineffective due to a minor copy/paste error.
adds 413af26 Use sam_itr_*()/etc and enable compiling with current htslib
adds 452dd14 Update dependencies and define _GNU_SOURCE only for bam_sort.o
adds 3181d5f Use htslib facilities instead of bam_parse_region() etc
adds 742b501 Make I/O redirection portable (to Linux)
adds 9838b1b Add test/merge/* test programs to main Makefile
adds 229e0ae Merge pull request #70, merge improvements
adds 8657d9a Limits -Q option (qual_scale) to sensible range 0 to 93.
adds 147afae bam_merge: get rid of asprintf warnings
adds b63021f bam_merge tests: fix warnings
adds feab370 Create xfreopen() utility instead of duplicating code
adds 04eeec5 Use kstring instead of asprintf()
adds 22247f1 Merge asprintf()->kstring rewrite and warning fixes (#161)
adds 3f92248 Fix buffer overflow
adds 7a87169 Use kstring instead of strndup()
adds ab05e1e Makes -r and -R read group filtering options both use settings.rghash
adds 73a00ad Ensures non-zero exit if -r / -R options fail to work.
adds 5fab219 Extant code in sam_view.c does not use Yoda conditions
adds c17f353 Merge read group filtering changes (PR #164)
adds 72cd75e Convert samtools stats to htslib
adds 07c0a23 Add Test files for stats
adds 80b25ca Merge pull request #174 from mp15/stats
adds 8054f37 Print dummy column for MAPQ for mpileup -s
adds fcc64e9 Disconnect clean-htslib from clean target
adds bfb0376 Fix compiler warning in stats
adds d23efe0 Enable tests for samtools stats
adds aeb923a Merge pull request #179 from mp15/stats
adds f189079 Rewrite bed_read
adds 91be501 Adds check to ensure bed_read worked, and exits non-zero if not.
adds 610db9c Stops samtools view from writing unmapped reads with -L (BED file) option
adds a5fabc5 Don't malloc the kstring_t; minor changes to the big comment
adds 11414ac Merge BED file parsing improvements (PR #165)
adds 99d13d8 add -U FILE to output unselected reads for pipelin
adds 6460586 Merge view -U option (PR #177), also adding it to the man page
adds 16c73e7 Makes samtools view subsampling option more random.
adds ea92f59 Merge view subsampling randomness (PR #167, fixes #160)
adds 06acafc Adds *~ (emacs backup files) and core to .gitignore.
adds e859892 Adds tests for samtools view.
adds 7b845e9 Merge branch 'develop' into develop_testing
adds c468057 Turns on CRAM region tests, now that CRAM indexing is supported.
adds c382302 Adds -L (BED file reading) tests.
adds 59171a3 Adds tests for the -t, -T and -B options.
adds f03d590 Adds more region tests.
adds abe156a Rolls converting back to SAM into run_view_test
adds 0ef36e8 Adds CRAM conversion using the MD5 REF_CACHE.
adds 62102f6 Merge branch 'develop' into develop_testing
adds d32c48f Strips out -x / -X tests as -X is deprecated and -x has been repurposed.
adds f3ac36f Adds more optional fields in test file, and more -R / -r checks.
adds 77cf9d4 Adds tests for the new -x tag stripping option.
adds 5c0d1e5 Adds tests for currently undocumented -m and -Q options.
adds ed12fe4 Adds some unaligned reads to the samtools view test file.
adds 8dc0e7b Minor changes to samtools view test output file names.
adds 4c7490b Adds tests for the -s (subsampling) and -@ (threads) options
adds 9490d1c Makes filter_sam filter @RG lines when filtering by read group.
adds f958e60 Adds comments to explain how the samtools view testing functions work.
adds 2db830d Changes *_compare functions to not call passed() or failed().
adds f77d2ab Removes dependency on gunzip
adds d858395 Merge branch 'develop' into develop_testing
adds 21534a1 Adds tests for 'samtools cat'
adds b659ed1 Adds more optional tags to alignment lines.
adds 79c4892 Add tests for bam2fq.
adds eadf538 Adds tests for samtools depad.
adds c80a3b0 Adds expected fail and unexpected pass.
adds ec3ffad Merge test cases from Rob Davies (PR #162)
adds b7ef33b Make xfail/xpass useable by other test subroutines
adds e6689c0 Make test_view() -@ tests portable to OS X
adds 4afab9a view: Free the header once finished
adds 3ad6995 Don't require an index for full-file merges
adds b44c5e4 merge,sort: Output BAM, not SAM. Build indexes
adds e35361b plot-bamstats: Fixes #183
adds f4e96f1 Adds support for outputting stats over the full input size distribution.
adds 2bab804 Merge pull request #184 from wtsi-hgi/features/unbounded-is
adds d2cad64 Further stats tests
adds 502d8dc Remove unusued 'total' functions.
adds 6951d73 Merge pull request #186 from wtsi-hgi/issues/warn-unusued-fn
adds 517d561 Merge branch 'origin/develop' into develop
adds 3518088 The @HD header is optional
adds 6557cbc Add "make testclean" target
adds c6e3d0b fall over if a bed file given as an option cannot be read
adds 402e355 Make stats.c's error() static like the others
adds 19d9fe0 Add print_error() and print_error_errno()
adds 5ab8804 Merge BED file option error checking (PR #77)
adds 8b268c0 Move CDF_MWU_TESTS switch closer to what it controls
adds 446c82a Reinstate old-API functions needed by Bio-SamTools Perl module
adds cb69971 Support for =X cigars in mpileup, exit on yet untreated cigars.
adds f9b1fdc Free all memory in sparse_isize_free
adds 3cbc80f stats: Support for =X cigars
adds cabd749 Fixes an issue with -i0 involving truncation of insert sizes.
adds a59e992 Added expected outputs for stats tests
adds d46e675 stats: Prevent nan on output
adds 3b739e9 bam_dup1() is now provided by htslib
adds 6c3bb9e Convert phase to htslib API
adds c2da7c1 Merge phase.c htslibification (PR #190)
adds ed70d9c Fixed script for parsing BLAST output
adds 267efc4 Fixed a few bugs in blast2sam.pl script, added POD documentation
adds 0c87b6e Merge blast2sam.pl improvements (PR #114)
adds 2917ccd Clean up merge memleaks
adds 802a6bf Silence -Wstrict-prototypes warnings
adds 8972694 Create header of common test functions
adds 1511278 Add split command to samtools
adds 6773e00 Add unit test for bam_split.c's count_rg
adds 179e432 Polish bam_split
adds 9274bbf Add unit test for bam_split.c's filter_header_rg
adds 901dc38 Restructure testing structure to dedupe
adds ec49dc4 Add unit test for bam_split.c's parse_args
adds 7e311b0 Fix dependencies for test/test.h
adds 13bc719 Write files based on the *basename* of the input file
adds a587da7 Merge split subcommand (PR #172)
adds eb2b309 mpileup: Long options; Custom DP,DV,DP,DP4 format fields on output
adds e9ea1ba Removed debugging exit in test.pl; Updated excl/incl long opts
adds 702dbd5 mpileup opts: -1,2 now recognised, --ff,rf on popular demand back
adds 1083db1 mpileup opts: Added forgotten --ff
adds 61cffe1 For your amusement, --ff goes with -2
adds d60458f Revert mpileup long options changes
adds 3939845 Use hts_set_threads() rather than bgzf_mt()
adds 1a46f21 Report sam_write1() and sam_close() errors
adds 80f09b4 Added mpileup tests
adds 578b207 Mpileup test in Makefile
adds a0b45d0 Avoid bashisms
adds 49f1859 Abort if an INIT command fails; dispose of _out file
adds e948340 Testclean and ignore temporary and output files
adds 38eda28 Merge mpileup tests (PR #187)
adds 69ab789 Fix long option has_arg inconsistencies
adds 3f6b1da mpileup: Absolute INFO/QS to allow incremental calling
adds 887e99d Cleanup split memleaks
adds e52fe3e Use kstring instead of POSIX 2008's strndup()
adds 1da3662 Merge split cleanups (PR #210)
adds 16b3d9c Remove our bgzip.c in favour of htslib/bgzip
adds 830473c Also clean test/test.o
adds 6f4376f Use getopt.h's descriptive constants in long options array
adds d9ed1b9 mpileup: support for BAM_CHARD_CLIP cigar
adds 93d2ede stats: Simplified usage of --GC-depth, reflen not required
adds 1972d96 Reformat usage for 80 columns
adds ffa59e7 To free unaccounted_header_name, it must have been malloced
adds 47e0bb0 Add code to separate out stdout and stderr in testing
adds e4d3791 Make merge take union of commandline and -b inputs and test merge code
adds e65f992 Add -b parameter to samtools merge manpage
adds ec6c929 Update samtools.1
adds eba6ecc Match style for FILE option
adds 586b747 Alternate syntax for samtools merge.
adds 6fd756f Alternate syntax for samtools merge in stderr message
adds eb500de Clarify list is not a literal
adds 6f42bf5 Match samtools merge manpage and stderr syntax
adds cbbd3a9 Merge branch 'patch-1' of https://github.com/SamStudio8/samtools into merge_unioninput
adds 7eb439e Make merge_usage()'s parameter directly understandable
adds 1d41868 Merge merge input and doc fixes, test stdout/stderr fixes (PRs #188, #202)
adds ba8da93 Fix getline memory leak in test_bam_translate
adds fecb1c8 Fix memory leak in test_rtrans_build
adds a55624f Fix memory leak in test_trans_tbl_init
adds 6cc9736 Add missing fclose of orig_stderr to test_bam_translate
adds e89ff5d Fix getline memory leak in test_filter_header_rg
adds e068ddc Fix getline missing fcloses in test_parse_args
adds e4baec7 Add missing frees to test_parse_args
adds 3a71203 Free char* in parsed_opts in test_parse_args
adds c433f19 No need to set len=0 before getline
adds f430ad3 Free all allocated names from count_RG
adds 8fc8247 Close orig_stderr *after* printing final error message
adds 39abb1f Merge test harness memory leaks (PR #200)
adds 40e4fde Fix calloc() type mismatch
adds 971d0e8 Prevent segfault when input file could not be opened
adds 8bd7048 Prevent segfault when input file could not be opened
adds 4162eb0 Test case fixed by htslib change
adds a5ffc51 stats: Check for zero-length cigars (e.g. 0D)
adds 813f310 Check for Usage output on stdout (ok) or stderr (expected failure)
adds f3b8f76 Migrate ideas from bam2fq from htslib and document
adds 7e811ce Miscellaneous code tweaks
adds e4b9925 Merge bam2fq improvements and documentation (PR #204)
adds f85fab7 Fixes `samtools sort` output to always be BAM
adds efe8857 Remove razip source code and remaining vestiges
adds 9dff552 Improves performance of `samtools merge` (slightly)
adds 1f3ab30 Removes '(forces -S)' from samtools view -T|t usage
adds f4e1e04 Updates documentation for `samtools view`
adds 3429f6e Tweak `samtools view` documentation formatting
adds de89a70 Merge view documentation updates (PR #218)
adds e20d0ce Ruthlessly tidied up the examples directory.
adds 501e9a7 Revert to ex1.sam.gz; fix mpileup command lines
adds 2c921cd Merge examples/ tidy up (PR #226)
adds 2f3b4a4 Add seq_cache_populate.pl
adds 3b292a4 Add seq_cache_populate.pl (PR #224), add it to "make install"
adds 71ab85c Reenable idxstats and convert to htslib
adds 08fc571 Update bam_index.o header dependencies
adds 4fbe2f0 Merge idxstats htslibification (PR #191)
adds 12c985f Call hts_set_fai_filename on the output fd too so that -T has a chance of working. This is one half of the fix necessary for https://github.com/samtools/samtools/issues/144
adds 5ae11c7 mpileup: Per-sample rather than cumulative QS. (experimental)
adds f85ac7d mpileup: Updated tests
adds bc0cae1 Merge branch 'develop' into QS-vs-PL
adds 6ec6b81 Merge QS-vs-PL branch into develop
adds 2455fd2 Add tests for making CRAM files using samtools view -t/-T
adds 6801e6d Add samtools index options to select BAI or CSI
adds 0e0ff87 Updated test harness to cope with CRAM now including MD and NM tags in output.
adds 0b8f96b mpileup: Reflect change in bcf_hdr_add_sample() usage
adds 6c80157 Add output mode parameter to bam_merge_core2 and bam_sort_core_ext
adds 2c2fb40 Overhaul samtools sort options and invocation
adds 7a2da96 mpileup: Long options
adds 1ad9f2e Create a print_usage() function for usage printing
adds b47cf4c Reformat usage to (mostly) fit in 80 columns
adds a5ba987 Minor rewording of usage to fit in 80 columns
adds a93a11d Deprecate `-S`, `-D`, `-V` in favour of `-t DP,DV,SP`
adds ce4cfc6 Fix long option has_arg inconsistencies
adds 7b8c24e some progress for mpileup documentation
adds 1bc231b Use getopt.h's descriptive constants in long options array
adds 6e0a670 Remove mpileup -M option, which has never been implemented
adds 159e846 Add lowercase synonyms for --VCF etc long options
adds ddbd14b Merge mpileup long options (PR #205)
adds 1ff7535 mpileup tests: Remove temporary hack, view -C -T now works
adds f891933 Merge mpileup test fix: Remove temporary hack, view -C -T now works
adds 8e0e91e Fix bug in merge for sorting large files
adds 222b94d Fix fixmate's properly paired check, add sam/cram output, add tests
adds f593548 Add mpileup --output option to redirect output to a file
adds fa9f902 Add mpileup -o FILE as a shorthand for --output
adds 773d3bc Updated calling section of samtools man page
adds a006f9d mpileup: New optional FORMAT/DPR and INFO/DPR annotations
adds b14b219 mpileup: Output symbolic <X> allele instead of VCF-incompatible X
adds 39f16d8 Save the right error text (fixes cut-and-pasto)
adds 5ec815e Added CRAM reference information and an example.
adds 0b94612 Report file opening failures rather than crashing
adds 978c2a8 Note explicitly that merge output remains sorted
adds 0248f39 Report errno for file opening failures
adds 11b4087 Implement bam2depth directly against the htslib API
adds 7ace6c2 Report index and region failures rather than crashing
adds 0f969b8 mpileup: Support for cigar operator "P", resolves #243
adds 17b06ad mpileup: Do not crash on non-existent files, resolves #244
adds 8030ea3 mpileup: Fix in DPR calculation - there can be
adds 5366fce Clear bcf_callret1_t to avoid segfault
adds f4320cd tview: Recover from incomplete fai files
adds 4735dbb Update documentation for samtools merge
adds 27d8e0c Fix idxstats error and add test
adds 57372fc mpileup: Support for cigar operation N
adds 5c3a553 add tests for samtools index with large chromosome
adds 9c4d66a Omit control files and README.md from release tarballs
adds 6684f78 Update license file
adds d366755 Add licensing boilerplate
adds 21680da Update copyright years to reflect historic changes
adds 62c3458 Add copyright notices and licensing boilerplate
adds 7006245 Add copyright notices and licensing boilerplate
adds 85cab3d Add copyright notices and licensing boilerplate
adds 02a6359 Update copyright years and reformat licensing boilerplate
adds 3ff81ed Update copyright years and reformat licensing boilerplate
adds a869c9a Fix copyright notices and reformat licensing boilerplate
adds 8da9ef2 Add copyright notices and licensing boilerplate
adds 0be3a71 Add copyright notices and licensing boilerplate
adds 293e8ce Reformat copyright notices and licensing boilerplate
adds 4363c1f Add copyright notices and licensing boilerplate
adds 1d7aecf Merge copyright notice and licensing boilerplate additions
adds fcb8af0 Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT
adds bbe85a9 Ensure installation directories are world-executable
adds e3f59f8 Man page minor edit and whitespace canonicalisation
adds 88f7ca9 plot-bamstats: better support for plots of single-read bams
adds 67a964d stats: Accept string flags with -f/F
adds 3ddba70 plot-bamstats: Generate summary html page
adds 9662d2d plot-bamstats: Use 0x1 rather than 0x2 flag to detect paired-end
adds 5943ad7 plot-bamstats: fixes in create_html and gz input
adds 433f887 Merge bug fixes for #183 and #262
adds c20d4bb Use "%s+htslib-%s" version format
adds ad732cd Add basic INSTALL and README files
adds 5370fe9 Release 1.0: first htslib-based samtools release
new 2192dda Merge version number bump from master branch
new e3d4eee fix DPR annotation
new a0254ac No need to initialise array anyway
new c8e1a2b stats: Compute checksum for names/seqs/quals
new 6099d57 Merge stats checksums
new f5288ca Replace bcftools+bcf_filter.sh with new vcf-miniview
new d0e4a6c Insulate test case from $GREP_OPTIONS
new 9579135 Update expected output with symbolic "<X>" alleles
new a7e257d Update QS values in expected output, and don't truncate them
new 258b4e6 Modified the mpileup tests to have local copies of appropriate reference sequences. All other tests already had this (but accidentally escaped in some circumstances).
new eeb4b22 Merge minimal MD5 reference area for mpileup tests
The 11 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitattributes | 5 +
.gitignore | 5 +-
AUTHORS | 10 +-
INSTALL | 36 +-
LICENSE | 33 +
Makefile | 178 +-
NEWS | 14 +
README | 5 +
README.md | 6 +-
bam.c | 263 +-
bam.h | 750 +-
bam2bcf.c | 529 +-
bam2bcf.h | 112 +-
bam2bcf_indel.c | 891 +-
bam2depth.c | 218 +-
bam_aux.c | 83 +-
bam_cat.c | 47 +-
bam_color.c | 226 +-
bam_endian.h | 52 +-
bam_flags.c | 35 +-
bam_import.c | 76 +-
bam_index.c | 143 +-
bam_lpileup.c | 315 +-
bam_lpileup.h | 57 +
bam_mate.c | 462 +-
bam_md.c | 705 +-
bam_plbuf.c | 67 +
bam_plbuf.h | 55 +
bam_plcmd.c | 1119 +-
bam_reheader.c | 109 +-
bam_rmdup.c | 327 +-
bam_rmdupse.c | 255 +-
bam_sort.c | 1550 +-
bam_split.c | 509 +
bam_stat.c | 150 +-
bam_tview.c | 760 +-
bam_tview.h | 70 +-
bam_tview_curses.c | 423 +-
bam_tview_html.c | 496 +-
bamshuf.c | 223 +-
bamtk.c | 172 +-
bedcov.c | 226 +-
bedidx.c | 322 +-
bgzip.c | 265 -
cut_target.c | 321 +-
errmod.c | 253 +-
errmod.h | 37 +-
examples/.gitignore | 1 +
examples/00README.txt | 40 +-
examples/Makefile | 50 -
examples/bam2bed.c | 51 -
examples/calDepth.c | 62 -
examples/chk_indel.c | 83 -
faidx.c | 39 +-
kaln.c | 2 +-
kaln.h | 2 +-
kprobaln.c | 2 +-
kprobaln.h | 2 +-
misc/HmmGlocal.java | 366 +-
misc/ace2sam.c | 384 +-
misc/blast2sam.pl | 204 +-
misc/bowtie2sam.pl | 97 +-
misc/export2sam.pl | 22 +-
misc/interpolate_sam.pl | 41 +-
misc/maq2sam.c | 262 +-
misc/md5.c | 2 +
misc/md5fa.c | 108 +-
misc/novo2sam.pl | 326 +-
misc/plot-bamstats | 487 +-
misc/psl2sam.pl | 60 +-
misc/r2plot.lua | 90 +-
misc/sam2vcf.pl | 85 +-
misc/samtools.pl | 506 +-
misc/seq_cache_populate.pl | 317 +
misc/soap2sam.pl | 91 +-
misc/varfilter.py | 304 +-
misc/vcfutils.lua | 1124 +-
misc/wgsim.c | 598 +-
misc/wgsim_eval.pl | 150 +-
misc/zoom2sam.pl | 73 +-
padding.c | 846 +-
phase.c | 1186 +-
razip.c | 142 -
sam.c | 137 +-
sam.h | 142 +-
sam_header.c | 154 +-
sam_header.h | 52 +-
sam_view.c | 1042 +-
sample.c | 171 +-
sample.h | 30 +-
samtools.1 | 908 +-
samtools.h | 39 +-
stats.c | 534 +-
stats_isize.c | 219 +
stats_isize.h | 83 +
test/dat/bam2fq.001.sam | 64 +
test/dat/cat.hdr | 25 +
test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468 | 1 +
test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437 | 1 +
test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4 | 1 +
test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b | 1 +
test/dat/depad.001.fa | 2 +
test/dat/depad.001.fa.fai | 1 +
test/dat/depad.001p.sam | 138 +
test/dat/depad.001u.sam | 138 +
test/dat/empty.expected | 0
test/dat/large_chrom.out | 6 +
test/dat/large_chrom.sam | 63 +
test/dat/large_chrom_bai_index.err | 1 +
test/dat/mpileup.1.sam | 1016 +
test/dat/mpileup.2.sam | 248 +
test/dat/mpileup.3.sam | 250 +
test/dat/mpileup.err.1 | 2 +
test/dat/mpileup.out.1 | 68 +-
test/dat/mpileup.out.2 | 1094 +-
test/dat/mpileup.out.4 | 527 +
test/dat/test_input_1_a.bam | Bin 0 -> 758 bytes
test/dat/test_input_1_a.bam.bai | Bin 0 -> 264 bytes
test/dat/test_input_1_a.sam | 28 +
test/dat/test_input_1_b.bam | Bin 0 -> 687 bytes
test/dat/test_input_1_b.bam.bai | Bin 0 -> 192 bytes
test/dat/test_input_1_b.sam | 24 +
test/dat/test_input_1_c.bam | Bin 0 -> 655 bytes
test/dat/test_input_1_c.bam.bai | Bin 0 -> 176 bytes
test/dat/test_input_1_c.sam | 22 +
test/dat/view.001.01.bed | 27 +
test/dat/view.001.02.bed | 22 +
test/dat/view.001.fa | 4 +
test/dat/view.001.fa.fai | 2 +
test/dat/view.001.sam | 62 +
test/dat/view.002.01.bed | 25 +
test/dat/view.002.02.bed | 30 +
test/dat/view.002.fa | 2 +
test/dat/view.002.fa.fai | 1 +
test/dat/view.002.sam | 83 +
test/dat/view.003.expected.sam | 39 +
test/dat/view.003.sam | 39 +
test/fixmate/1_coord_sort.sam.expected | 0
test/fixmate/1_coord_sort.sam.expected.err | 2 +
..._overflow.sam => 2_isize_overflow.sam.expected} | 12 +-
test/fixmate/3_reverse_read_pp_lt.sam | 5 +
test/fixmate/3_reverse_read_pp_lt.sam.expected | 5 +
test/fixmate/4_reverse_read_pp_equal.sam | 5 +
test/fixmate/4_reverse_read_pp_equal.sam.expected | 5 +
test/idxstats/test_input_1_a.bam.expected | 5 +
test/idxstats/test_input_1_a.bam.expected.err | 0
test/merge/.gitignore | 6 +
test/merge/2.merge.expected.bam | Bin 0 -> 1181 bytes
test/merge/3.merge.expected.bam | Bin 0 -> 1199 bytes
test/merge/3.merge.expected.err | 5 +
test/merge/test_3.fofn | 2 +
test/merge/test_bam_translate.c | 591 +
test/merge/test_header.sam | 11 +
test/merge/test_pretty_header.c | 87 +
test/merge/test_rtrans_build.c | 118 +
test/merge/test_trans_tbl_init.c | 471 +
test/mpileup/.gitignore | 11 +
test/mpileup/1read.bam | Bin 0 -> 525 bytes
test/mpileup/1read.sam | 1 +
test/mpileup/anomalous.sam | 6 +
test/mpileup/c1#ID.bam | Bin 0 -> 293 bytes
test/mpileup/c1#ID2.bam | Bin 0 -> 377 bytes
test/mpileup/c1#clip.bam | Bin 0 -> 265 bytes
test/mpileup/c1#pad1.bam | Bin 0 -> 299 bytes
test/mpileup/c1#pad2.bam | Bin 0 -> 349 bytes
test/mpileup/c1#pad3.bam | Bin 0 -> 382 bytes
test/mpileup/c1.fa | 4 +
test/mpileup/c1.fa.fai | 2 +
test/mpileup/ce#5b.bam | Bin 0 -> 557 bytes
test/mpileup/ce#5b.bam.bai | Bin 0 -> 416 bytes
test/mpileup/ce#5b.cram | Bin 0 -> 13183 bytes
test/mpileup/ce#5b.cram.crai | Bin 0 -> 75 bytes
test/mpileup/ce#5b.sam | 12 +
test/mpileup/ce#large_seq.bam | Bin 0 -> 345315 bytes
test/mpileup/ce#unmap.bam | Bin 0 -> 233 bytes
test/mpileup/ce#unmap1.bam | Bin 0 -> 896 bytes
test/mpileup/ce#unmap2.bam | Bin 0 -> 1344 bytes
test/mpileup/ce.fa | 20803 +++++++++++++++++++
test/mpileup/ce.fa.fai | 7 +
test/mpileup/deep.sam | 9001 ++++++++
test/mpileup/expected/1.out.xz | Bin 0 -> 1336220 bytes
test/mpileup/expected/10.out | 40 +
test/mpileup/expected/11.out | 9 +
test/mpileup/expected/12.out | 9 +
test/mpileup/expected/13.out | 4101 ++++
test/mpileup/expected/14.out | 4101 ++++
test/mpileup/expected/15.out | 4101 ++++
test/mpileup/expected/16.out | 4101 ++++
test/mpileup/expected/17.out | 4101 ++++
test/mpileup/expected/18.out | 4101 ++++
test/mpileup/expected/19.out | 4101 ++++
test/mpileup/expected/2.out | 0
test/mpileup/expected/20.out | 4101 ++++
test/mpileup/expected/21.out | 4101 ++++
test/mpileup/expected/22.out | 4101 ++++
test/mpileup/expected/23.out | 150 +
test/mpileup/expected/24.out | 150 +
test/mpileup/expected/25.out | 150 +
test/mpileup/expected/26.out | 100 +
test/mpileup/expected/27.out | 100 +
test/mpileup/expected/28.out | 4101 ++++
test/mpileup/expected/29.out | 0
test/mpileup/expected/3.out | 0
test/mpileup/expected/30.out | 100 +
test/mpileup/expected/31.out | 100 +
test/mpileup/expected/32.out | 100 +
test/mpileup/expected/33.out | 12 +
test/mpileup/expected/34.out | 12 +
test/mpileup/expected/35.out | 3397 +++
test/mpileup/expected/37.out | 4101 ++++
test/mpileup/expected/38.out | 102 +
test/mpileup/expected/39.out | 11 +
test/mpileup/expected/4.out | 101 +
test/mpileup/expected/40.out | 84 +
test/mpileup/expected/41.out | 21 +
test/mpileup/expected/42.out | 0
test/mpileup/expected/43.out | 3893 ++++
test/mpileup/expected/44.out | 3893 ++++
test/mpileup/expected/45.out | 4097 ++++
test/mpileup/expected/46.out | 4097 ++++
test/mpileup/expected/47.out | 1 +
test/mpileup/expected/48.out | 4104 ++++
test/mpileup/expected/49.out | 4104 ++++
test/mpileup/expected/5.out | 10 +
test/mpileup/expected/50.out | 4104 ++++
test/mpileup/expected/51.out | 4104 ++++
test/mpileup/expected/52.out | 1 +
test/mpileup/expected/53.out | 1 +
test/mpileup/expected/54.out | 1 +
test/mpileup/expected/55.out | 1 +
test/mpileup/expected/56.out | 1 +
test/mpileup/expected/57.out | 1 +
test/mpileup/expected/58.out | 1 +
test/mpileup/expected/59.out | 1 +
test/mpileup/expected/6.out | 10 +
test/mpileup/expected/60.out | 0
test/mpileup/expected/61.out | 1 +
test/mpileup/expected/62.out | 0
test/mpileup/expected/63.out | 1 +
test/mpileup/expected/64.out | 0
test/mpileup/expected/65.out | 1 +
test/mpileup/expected/66.out | 0
test/mpileup/expected/67.out | 1 +
test/mpileup/expected/68.out | 0
test/mpileup/expected/69.out | 0
test/mpileup/expected/7.out | 10 +
test/mpileup/expected/70.out | 1 +
test/mpileup/expected/71.out | 1 +
test/mpileup/expected/72.out | 0
test/mpileup/expected/73.out | 1 +
test/mpileup/expected/74.out | 0
test/mpileup/expected/75.out | 1 +
test/mpileup/expected/76.out | 4101 ++++
test/mpileup/expected/77.out | 4101 ++++
test/mpileup/expected/8.out | 5 +
test/mpileup/expected/9.out | 10 +
test/mpileup/indels.sam | 9 +
test/mpileup/md5/02099b2aad2cfe707759353724fb40ae | 1 +
test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d | 1 +
test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de | 1 +
test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc | 1 +
test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 | 1 +
test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e | 1 +
test/mpileup/mpileup-E.bam | Bin 0 -> 280 bytes
test/{dat => mpileup}/mpileup.1.bam | Bin
test/mpileup/mpileup.1.bam.bai | Bin 0 -> 776 bytes
test/{dat => mpileup}/mpileup.2.bam | Bin
test/{dat => mpileup}/mpileup.3.bam | Bin
test/{dat => mpileup}/mpileup.ref.fa | 0
test/{dat => mpileup}/mpileup.ref.fa.fai | 0
test/mpileup/mpileup.reg | 144 +
test/mpileup/overlap50.sam | 5 +
test/mpileup/overlapIllumina.bam | Bin 0 -> 583 bytes
test/mpileup/regions | 10 +
test/mpileup/regression.sh | 157 +
test/mpileup/xx#minimal.bam | Bin 0 -> 215 bytes
test/mpileup/xx#triplet.bam | Bin 0 -> 247 bytes
test/mpileup/xx.fa | 5 +
test/mpileup/xx.fa.fai | 2 +
test/split/.gitignore | 4 +
test/split/test_count_rg.c | 124 +
test/split/test_expand_format_string.c | 124 +
test/split/test_filter_header_rg.c | 191 +
test/split/test_parse_args.c | 215 +
test/stat/1.stats.expected | 302 +
test/stat/1_map_cigar.sam | 5 +
test/stat/2.stats.expected | 302 +
test/stat/2_equal_cigar_full_seq.sam | 5 +
test/stat/3.stats.expected | 265 +
test/stat/3_map_cigar_equal_seq.sam | 5 +
test/stat/4.stats.expected | 302 +
test/stat/4_X_cigar_full_seq.sam | 5 +
test/stat/5.stats.expected | 304 +
test/stat/5_insert_cigar.sam | 5 +
test/stat/6.stats.expected | 304 +
test/stat/test.fa | 3 +
test/stat/test.fa.fai | 1 +
test/test.c | 53 +
COPYING => test/test.h | 28 +-
test/test.pl | 1980 +-
test/tview/test_get_rg_sample.c | 81 +
test/vcf-miniview.c | 115 +
302 files changed, 148612 insertions(+), 10984 deletions(-)
create mode 100644 LICENSE
create mode 100644 README
create mode 100644 bam_lpileup.h
create mode 100644 bam_plbuf.c
create mode 100644 bam_plbuf.h
create mode 100644 bam_split.c
delete mode 100644 bgzip.c
delete mode 100644 examples/Makefile
delete mode 100644 examples/bam2bed.c
delete mode 100644 examples/calDepth.c
delete mode 100644 examples/chk_indel.c
create mode 100755 misc/seq_cache_populate.pl
delete mode 100644 razip.c
create mode 100644 stats_isize.c
create mode 100644 stats_isize.h
create mode 100644 test/dat/bam2fq.001.sam
create mode 100644 test/dat/cat.hdr
create mode 100644 test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468
create mode 100644 test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437
create mode 100644 test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4
create mode 100644 test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b
create mode 100644 test/dat/depad.001.fa
create mode 100644 test/dat/depad.001.fa.fai
create mode 100644 test/dat/depad.001p.sam
create mode 100644 test/dat/depad.001u.sam
create mode 100644 test/dat/empty.expected
create mode 100644 test/dat/large_chrom.out
create mode 100644 test/dat/large_chrom.sam
create mode 100644 test/dat/large_chrom_bai_index.err
create mode 100644 test/dat/mpileup.1.sam
create mode 100644 test/dat/mpileup.2.sam
create mode 100644 test/dat/mpileup.3.sam
create mode 100644 test/dat/mpileup.err.1
create mode 100644 test/dat/mpileup.out.4
create mode 100644 test/dat/test_input_1_a.bam
create mode 100644 test/dat/test_input_1_a.bam.bai
create mode 100644 test/dat/test_input_1_a.sam
create mode 100644 test/dat/test_input_1_b.bam
create mode 100644 test/dat/test_input_1_b.bam.bai
create mode 100644 test/dat/test_input_1_b.sam
create mode 100644 test/dat/test_input_1_c.bam
create mode 100644 test/dat/test_input_1_c.bam.bai
create mode 100644 test/dat/test_input_1_c.sam
create mode 100644 test/dat/view.001.01.bed
create mode 100644 test/dat/view.001.02.bed
create mode 100644 test/dat/view.001.fa
create mode 100644 test/dat/view.001.fa.fai
create mode 100644 test/dat/view.001.sam
create mode 100644 test/dat/view.002.01.bed
create mode 100644 test/dat/view.002.02.bed
create mode 100644 test/dat/view.002.fa
create mode 100644 test/dat/view.002.fa.fai
create mode 100644 test/dat/view.002.sam
create mode 100644 test/dat/view.003.expected.sam
create mode 100644 test/dat/view.003.sam
create mode 100644 test/fixmate/1_coord_sort.sam.expected
create mode 100644 test/fixmate/1_coord_sort.sam.expected.err
copy test/fixmate/{2_isize_overflow.sam => 2_isize_overflow.sam.expected} (64%)
create mode 100644 test/fixmate/3_reverse_read_pp_lt.sam
create mode 100644 test/fixmate/3_reverse_read_pp_lt.sam.expected
create mode 100644 test/fixmate/4_reverse_read_pp_equal.sam
create mode 100644 test/fixmate/4_reverse_read_pp_equal.sam.expected
create mode 100644 test/idxstats/test_input_1_a.bam.expected
create mode 100644 test/idxstats/test_input_1_a.bam.expected.err
create mode 100644 test/merge/.gitignore
create mode 100644 test/merge/2.merge.expected.bam
create mode 100644 test/merge/3.merge.expected.bam
create mode 100644 test/merge/3.merge.expected.err
create mode 100644 test/merge/test_3.fofn
create mode 100644 test/merge/test_bam_translate.c
create mode 100644 test/merge/test_header.sam
create mode 100644 test/merge/test_pretty_header.c
create mode 100644 test/merge/test_rtrans_build.c
create mode 100644 test/merge/test_trans_tbl_init.c
create mode 100644 test/mpileup/.gitignore
create mode 100644 test/mpileup/1read.bam
create mode 100644 test/mpileup/1read.sam
create mode 100644 test/mpileup/anomalous.sam
create mode 100644 test/mpileup/c1#ID.bam
create mode 100644 test/mpileup/c1#ID2.bam
create mode 100644 test/mpileup/c1#clip.bam
create mode 100644 test/mpileup/c1#pad1.bam
create mode 100644 test/mpileup/c1#pad2.bam
create mode 100644 test/mpileup/c1#pad3.bam
create mode 100644 test/mpileup/c1.fa
create mode 100644 test/mpileup/c1.fa.fai
create mode 100644 test/mpileup/ce#5b.bam
create mode 100644 test/mpileup/ce#5b.bam.bai
create mode 100644 test/mpileup/ce#5b.cram
create mode 100644 test/mpileup/ce#5b.cram.crai
create mode 100644 test/mpileup/ce#5b.sam
create mode 100644 test/mpileup/ce#large_seq.bam
create mode 100644 test/mpileup/ce#unmap.bam
create mode 100644 test/mpileup/ce#unmap1.bam
create mode 100644 test/mpileup/ce#unmap2.bam
create mode 100644 test/mpileup/ce.fa
create mode 100644 test/mpileup/ce.fa.fai
create mode 100644 test/mpileup/deep.sam
create mode 100644 test/mpileup/expected/1.out.xz
create mode 100644 test/mpileup/expected/10.out
create mode 100644 test/mpileup/expected/11.out
create mode 100644 test/mpileup/expected/12.out
create mode 100644 test/mpileup/expected/13.out
create mode 100644 test/mpileup/expected/14.out
create mode 100644 test/mpileup/expected/15.out
create mode 100644 test/mpileup/expected/16.out
create mode 100644 test/mpileup/expected/17.out
create mode 100644 test/mpileup/expected/18.out
create mode 100644 test/mpileup/expected/19.out
create mode 100644 test/mpileup/expected/2.out
create mode 100644 test/mpileup/expected/20.out
create mode 100644 test/mpileup/expected/21.out
create mode 100644 test/mpileup/expected/22.out
create mode 100644 test/mpileup/expected/23.out
create mode 100644 test/mpileup/expected/24.out
create mode 100644 test/mpileup/expected/25.out
create mode 100644 test/mpileup/expected/26.out
create mode 100644 test/mpileup/expected/27.out
create mode 100644 test/mpileup/expected/28.out
create mode 100644 test/mpileup/expected/29.out
create mode 100644 test/mpileup/expected/3.out
create mode 100644 test/mpileup/expected/30.out
create mode 100644 test/mpileup/expected/31.out
create mode 100644 test/mpileup/expected/32.out
create mode 100644 test/mpileup/expected/33.out
create mode 100644 test/mpileup/expected/34.out
create mode 100644 test/mpileup/expected/35.out
create mode 100644 test/mpileup/expected/37.out
create mode 100644 test/mpileup/expected/38.out
create mode 100644 test/mpileup/expected/39.out
create mode 100644 test/mpileup/expected/4.out
create mode 100644 test/mpileup/expected/40.out
create mode 100644 test/mpileup/expected/41.out
create mode 100644 test/mpileup/expected/42.out
create mode 100644 test/mpileup/expected/43.out
create mode 100644 test/mpileup/expected/44.out
create mode 100644 test/mpileup/expected/45.out
create mode 100644 test/mpileup/expected/46.out
create mode 100644 test/mpileup/expected/47.out
create mode 100644 test/mpileup/expected/48.out
create mode 100644 test/mpileup/expected/49.out
create mode 100644 test/mpileup/expected/5.out
create mode 100644 test/mpileup/expected/50.out
create mode 100644 test/mpileup/expected/51.out
create mode 100644 test/mpileup/expected/52.out
create mode 100644 test/mpileup/expected/53.out
create mode 100644 test/mpileup/expected/54.out
create mode 100644 test/mpileup/expected/55.out
create mode 100644 test/mpileup/expected/56.out
create mode 100644 test/mpileup/expected/57.out
create mode 100644 test/mpileup/expected/58.out
create mode 100644 test/mpileup/expected/59.out
create mode 100644 test/mpileup/expected/6.out
create mode 100644 test/mpileup/expected/60.out
create mode 100644 test/mpileup/expected/61.out
create mode 100644 test/mpileup/expected/62.out
create mode 100644 test/mpileup/expected/63.out
create mode 100644 test/mpileup/expected/64.out
create mode 100644 test/mpileup/expected/65.out
create mode 100644 test/mpileup/expected/66.out
create mode 100644 test/mpileup/expected/67.out
create mode 100644 test/mpileup/expected/68.out
create mode 100644 test/mpileup/expected/69.out
create mode 100644 test/mpileup/expected/7.out
create mode 100644 test/mpileup/expected/70.out
create mode 100644 test/mpileup/expected/71.out
create mode 100644 test/mpileup/expected/72.out
create mode 100644 test/mpileup/expected/73.out
create mode 100644 test/mpileup/expected/74.out
create mode 100644 test/mpileup/expected/75.out
create mode 100644 test/mpileup/expected/76.out
create mode 100644 test/mpileup/expected/77.out
create mode 100644 test/mpileup/expected/8.out
create mode 100644 test/mpileup/expected/9.out
create mode 100644 test/mpileup/indels.sam
create mode 100644 test/mpileup/md5/02099b2aad2cfe707759353724fb40ae
create mode 100644 test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d
create mode 100644 test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de
create mode 100644 test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc
create mode 100644 test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1
create mode 100644 test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e
create mode 100644 test/mpileup/mpileup-E.bam
rename test/{dat => mpileup}/mpileup.1.bam (100%)
create mode 100644 test/mpileup/mpileup.1.bam.bai
rename test/{dat => mpileup}/mpileup.2.bam (100%)
rename test/{dat => mpileup}/mpileup.3.bam (100%)
copy test/{dat => mpileup}/mpileup.ref.fa (100%)
copy test/{dat => mpileup}/mpileup.ref.fa.fai (100%)
create mode 100644 test/mpileup/mpileup.reg
create mode 100644 test/mpileup/overlap50.sam
create mode 100644 test/mpileup/overlapIllumina.bam
create mode 100644 test/mpileup/regions
create mode 100755 test/mpileup/regression.sh
create mode 100644 test/mpileup/xx#minimal.bam
create mode 100644 test/mpileup/xx#triplet.bam
create mode 100644 test/mpileup/xx.fa
create mode 100644 test/mpileup/xx.fa.fai
create mode 100644 test/split/.gitignore
create mode 100644 test/split/test_count_rg.c
create mode 100644 test/split/test_expand_format_string.c
create mode 100644 test/split/test_filter_header_rg.c
create mode 100644 test/split/test_parse_args.c
create mode 100644 test/stat/1.stats.expected
create mode 100644 test/stat/1_map_cigar.sam
create mode 100644 test/stat/2.stats.expected
create mode 100644 test/stat/2_equal_cigar_full_seq.sam
create mode 100644 test/stat/3.stats.expected
create mode 100644 test/stat/3_map_cigar_equal_seq.sam
create mode 100644 test/stat/4.stats.expected
create mode 100644 test/stat/4_X_cigar_full_seq.sam
create mode 100644 test/stat/5.stats.expected
create mode 100644 test/stat/5_insert_cigar.sam
create mode 100644 test/stat/6.stats.expected
create mode 100644 test/stat/test.fa
create mode 100644 test/stat/test.fa.fai
create mode 100644 test/test.c
rename COPYING => test/test.h (61%)
create mode 100644 test/tview/test_get_rg_sample.c
create mode 100644 test/vcf-miniview.c
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