[med-svn] [SCM] samtools annotated tag, st-final, created. st-final
samtools
lh3 at sanger.ac.uk
Sat Mar 30 09:17:15 UTC 2013
The annotated tag, st-final has been created
at 1a17f35faf7f3f43e52db1702aafe3f77b33ca70 (tag)
tagging 7e7b21944f4d89442896d1618f65c22b509c0326 (commit)
tagged by Heng Li
on Thu Mar 29 14:14:52 2012 -0400
- Shortlog ------------------------------------------------------------
Heng Li (546):
Create trunk copy
* Merge from branches/dev/
* merge from branches/dev/
* samtools-0.1.1-19
update documentation and ChangeLog
add a script to convert novo alignment to SAM
convert ZOOM to SAM
Script for filtering indel results
Release SAMtools-0.1.2
* samtools-0.1.2-1
* samtools-0.1.2-3
fixed a potential memory problem in indexing
fixed a bug in generating tag AM
* output max mapping quality in indel line
* samtools-0.1.2-6
* samtools-0.1.2-7
* samtools-0.1.2-7
* move indel_filter.pl to samtools.pl
* samtools-0.1.2-9
* wgsim-0.2.0
* wgsim: added a note
* wgsim-0.2.1
* wgsim-0.2.2
* wgsim-0.2.3
* samtools-0.1.2-10
* samtools-0.1.2-11
* samtools-0.1.2-12
* samtools-0.1.2-13
* samtools-0.1.2-14
* samtools-0.1.2-15
added bam_stat.o to Makefile.lite
* soap2sam.pl-0.1.2
* samtools-0.1.2-16
* samtools-0.1.2-17
rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time...
* samtools-0.1.2-18
* samtools-0.1.2-19
* samtools-0.1.2-20
make the script robust to the bugs in SOAP-2.1.7
* samtools-0.1.2-21
* fixed the problem in the example alignment due to the bug in fixmate
* samtools-0.1.2-22
* samtools-0.1.2-23
* samtools-0.1.2-24
update ChangeLog from "svn log"
* samtools-0.1.2-25
* samtools.pl-0.1.1
proposed NEWS for the new release (have not yet)
* samtools-0.1.2-26
* samtools-0.1.2-27
convert NCBI-BLASTN to SAM
prepare for release 0.1.3
* samtools-0.1.2-28
Release samtools-0.1.3
a missing file in Makefile.lite
* samtools-0.1.3-1
* samtools-0.1.3-2 (r239)
* samtools-0.1.3-3 (r240)
* samtools-0.1.3-4 (r242)
* samtools-0.1.3-5 (r243)
* samtools-0.1.3-6 (r244)
* samtools-0.1.3-7 (r246)
fixed various issues about the GNU building scripts
update INSTALL
improve large file support in compilation
added missing files
* samtools-0.1.3-8 (r251)
* samtools-0.1.3-9 (r256)
* samtools-0.1.3-10 (r257)
* samtools-0.1.3-11 (r258)
* samtools-0.1.3-12 (r259)
update Makefile.am
* samtools-0.1.3-13 (r260)
* samtools-0.1.3-14 (r262)
* samtools-0.1.3-15 (r266)
* samtools-0.1.3-16 (r267)
* samtools-0.1.3-17 (r271)
change a parameter. It does nothing
* samtools-0.1.3-18 (r273)
* samtools-0.1.3-19 (r275)
* samtools-0.1.3-20 (r276)
* samtools-0.1.3-21 (286)
Added a note to the manual. Currently SAMtools used unaligned words in
* samtools-0.1.3-22 (r293)
added a missing header file
* samtools-0.1.3-23 (r295)
* samtools-0.1.3-24 (r296)
Release samtools-0.1.4
* samtools-0.1.4-1 (r304)
Script for paired-end pileup, contributed by Stephen Montgomery.
* minor changes to bgzf: return NULL if fd == -1
* samtools.pl-0.2.0
* samtools.pl-0.2.1
* in snpFilter, suppress non-SNP sites
* samtools.pl-0.2.2
* samtools-0.1.4-2 (r316)
* samtools.pl-0.2.3
* samtools.pl-0.3.0
* samtools.pl-0.3.1
a little bit code cleanup
just typo. no real change
fixed a typo
* samtools.pl-0.3.2 (r322)
* samtools-0.1.4-3 (r324)
* samtools-0.1.4-4 (r325)
Unfinished
* added zlib-1.2.3 as razip requires that
* update Makefile
* updated novoalign converter by Colin Hercus et al.
update information...
* samtools-0.1.4-5 (r3310
fixed minor things in Makefile
update ChangeLog
* samtools-0.1.4-6 (r334)
remove zlib for simplification...
* no changes to samtools itself
* samtools-0.1.4-7 (r337)
* samtools-0.1.4-8 (r338)
update INSTALL
* samtools-0.1.4-9 (r340)
* samtools-0.1.4-10 (r341)
added an example of calculating read depth
nothing really
added more comments
* samtools-0.1.4-11 (r346)
* samtools-0.1.4-12 (r347)
* samtools-0.1.4-13 (r350)
* samtools-0.1.4-13 (r351)
* samtools-0.1.4-15 (r354)
* open a file at FTP
this is the header file
fixed bugs in knetfile.*
* samtools-0.1.4-16 (r360)
* samtools-0.1.4-17 (r361)
write changelog
* samtools-0.1.4-18 (r363)
* samtools-0.1.4-19 (r364)
* samtools-0.1.4-20 (r365)
minor changes to knetfile: invalid fd equals -1 rather than 0
reduce the chance of blocking in FTP connection
* samtools-0.1.4-21 (r368)
* samtools-0.1.4-22 (r369)
update documentation
* samtools-0.1.4-23 (r372)
Release samtools-0.1.5
Release samtools-0.1.5a (for compatibility with Bio::DB::Sam)
Release samtools-0.1.5b (BUG! so embarrassing!)
Release samtools-0.1.5c (fixed a bug in piping)
* samtools-0.1.5-1 (r390)
* samtools-0.1.5-2 (r391)
Remove the warning in tview
* samtools-0.1.5-3 (r393)
* samtools-0.1.5-4 (r394)
* samtools-0.1.5-5 (r395)
* move bam_lite.c to bam-lite
* samtools-0.1.5-6 (r402)
* samtools-0.1.5-7 (r403)
* samtools-0.1.5-8 (r404)
* samtools-0.1.5-9 (r405)
Sorry. The old Makefile is for PDCurses...
* samtools-0.1.5-10 (r407)
* samtools-0.1.5-11 (r408)
do not include knetfile.h when _USE_KNETFILE is not defined
Implemented Boyer-Moore search in the kstring library.
fixed a compiling error (thank Ken for fixing it)
* samtools-0.1.5-12 (r415)
* samtools-0.1.5-17 (r416)
* samtools-0.1.5-14 (r417)
skip @header lines in SAM
* samtools-0.1.5-15 (r419)
do not set "read 1" if reads are not mapped in the PE mode of maq
* samtools-0.1.5-16 (r421)
* samtools-0.1.5-17 (r422)
convert BLAT psl to SAM.
* samtools-0.1.5-18 (r423)
compatible with Windows binary files
* samtools-0.1.5-19 (r426)
* samtools-0.1.5-20 (r427)
simplify MinGW Makefile
* samtools-0.1.5-21 (r428)
add comments
replace the GnuWin32 version of libz.a with my own build with MinGW.
* samtools-0.1.5-22 (r432)
* tried to fixed the buggy FTP random access in Windows. FAILED.
* samtools-0.1.5-23 (r434)
* samtools-0.1.5-24 (r435)
fixed two minor bugs (suggested by Tim M Storm)
fixed a SERIOUS bug in setting 0x20 flag
* samtools-0.1.5-25 (r436)
* samtools-0.1.5-26 (r442)
* samtools-0.1.5-27 (r443)
* samtools-0.1.5-28 (r444)
*
* samtools-0.1.5-30 (r447)
* samtools-0.1.5-31 (r448)
* samtools-0.1.5-32 (r449)
* samtools-0.1.5-33 (r450)
* samtools-0.1.5-34 (r451)
Release samtools-0.1.6
* samtools-0.1.6-2 (r457)
* samtools-0.1.6-2 (r458)
* samtools-0.1.6-4 (r459)
fixed a formatting issue
* samtools-0.1.6-5 (r462)
* samtools-0.1.6-6 (r466)
* samtools-0.1.6-7 (r468)
* samtools-0.1.6-9 (r469)
* samtools-0.1.6-9 (r470)
Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
Clarify the meaning of a region like "chr2:1,000,000".
Unfinished modification. Please do not use this revision...
* samtools-0.1.6-11 (r477)
* samtools-0.1.6-12 (r478)
* samtools-0.1.6-13 (r479)
added a small unitity to parse SRA XML files
* samtools-0.1.6-14 (r480)
* samtools-0.1.6-15 (r482)
* samtools-0.1.6-16 (r483)
* samtools-0.1.6-17 (r484)
* This revision is SERIOUSLY BUGGY. Please NOT use it.
* BUGGY VERSION. Please NOT use it.
* BUGGY VERSION
* BUGGY VERSION
* samtools-0.1.6-18 (r493)
* samtools-0.1.6-19 (r494)
* samtools-0.1.6-21 (r508)
* samtools-0.1.6-22 (r509)
Release samtools-0.1.7 (r510)
Fixed a bug in compiling razip
Update Makefile.mingw for the same reason
* samtools-0.1.7-1 (r515)
another example program
* samtools-0.1.7-2 (r520)
* samtools-0.1.7-3 (r521)
* samtools-0.1.7-4 (r522)
* samtools-0.1.7-5 (r528)
* samtools-0.1.7-6
added a hidden option in pileup to output the base position (for Erin)
Updated export2sam.pl by Chris Saunders from Illumina.
* samtools-0.1.7-7 (r584)
* samtools-0.1.7-8 (r585)
* samtools-0.1.7-9 (r586)
* samtools-0.1.7-10 (r587)
* samtools-0.1.7-11 (r588)
* samtools-0.1.7-12 (r589)
* samtools-0.1.7-13 (r590)
* samtools-0.1.7-14 (r591)
* samtools-0.1.7-15 (r592)
rename iterf as iter
fixed a bug for unmapped sequences in indexing
* samtools-0.1.7-16 (r595)
* samtools-0.1.7-17 (r596)
added Makefile targets to compile shared/dynamic library
minor fix. No actual effect.
change printf() to puts in exporting
fixed a minor bug in indexing
fixed a minor bug in idxstats
* samtools-.1.7-18 (r605)
removed a debugging example
* samtools-0.1.7-r607
* make tview more friendly
make pileup work with CIGAR with I/D at the beginning or in the end
change the command line option of pileup
fixed a bug in sorting when output to stdout (by Peter Chines)
fixed a compiling issue for Windows
Release samtools-0.1.8
* samtools-0.1.8-1 (r615)
* added mutli-sample framework. It is not working, yet.
* samtools-0.1.8-2 (r617)
* preliminary multisample SNP caller.
* samtools-0.1.8-3 (r627)
calculate posterior allele frequency
added an alternative prior
added the format column
another minor fix to mpileup
posterior expectation FINALLY working. I am so tired...
minor tweaks
minor changes
* samtools-0.1.8-6 (r638)
* samtools-0.1.8-7 (r639)
NOT ready yet. Going to make further changes...
supposedly this is THE correct implementation, but more testing is needed
* fixed a STUPID bug, which cost me a lot of time.
* samtools-0.1.8-8 (r644)
Generate binary VCF
* samtools-0.1.8-9 (r649)
fixed a bug
fixed a bug in bcf reader
fixed a memory leak
missing a column in VCF output...
* fixed a bug
* samtools-0.1.8-10 (r658)
fixed another minor bug
move bcftools to samtools
fixed compilation error
added more examples
spec
* allow to set min base q
* added prelimiary VCF parser (not finished)
unfinished vcf parser
minor
* the code base is stablized again.
* samtools-0.1.8-11 (r672)
Fisher's exact test
* Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
* bcftools: add HWE (no testing for now)
reimplement incomplete gamma functions. no copy-paste
* test depth, end distance and HWE
perform single-tail test for ED4
help messages
* improved kstring (added kstrtok)
* fixed a bug in kstrtok at kstring.c
* parse PL
do not print refname if file is converted from VCF
fixed an issue in parsing integer
* a numerically stable method to calculate z_{jk}
faster for large sample size (in principle)
use float for QUAL
* write a little more VCF header
allow to read the prior from the error output. EM iteration is working.
added revised MAQ error model
* use the revised MAQ error model for mpileup
remove VCF output in mpileup
* samtools-0.1.8-12 (r692)
print QUAL as floating numbers
change the default correlation coefficient
added regularized incomplete beta function
* samtools-0.1.8-13 (r698)
fixed a bug in calculating the t statistics
* rename vcfout.c as call1.c
z' and z'' can be calculated
preliminary contrast variant caller
Utilities for processing VCF
more commands for my own uses
Write the correct ALT and PL in the SNP calling mode.
Do not compile _BCF_QUAD by default
* fixed bugs in parsing VCF
fixed another problem
SNP calling from the GL field
* changed 3.434 to 4.343 (typo!)
quite a lot changes to the contrast caller, but I still feel something is missing...
* samtools-0.1.8-13 (r715)
* aggressive gapped aligner is implemented in calmd.
minor changes. It is BUGGY now!
fixed a bug in realignment
fixed a minor issue
fixed a bug in realignment
dynamic band width in realignment
* convert BCF to QCALL input
* added varFilter to vcfutils.pl
* samtools-0.1.8-14 (r727)
* fixed a bug in razip: -c will delete the input file
* fixed a bug in capQ
fixed a bug in indexing
* put n_smpl to "bcf1_t" to simplify API a little
* added comments
hapmap2vcf convertor
convert UCSC SNP SQL dump to VCF
improve qstats by checking the alleles as well
* merge files region-by-region. work on small examples but more tests are needed.
* samtools-0.1.8-15 (r379)
...
A little code cleanup. Now the forward and backback algorithms give
More comments. This version seems working, but something is a little weird...
* fixed that weird issue.
fixed a bug in banded DP
more comments
improve numerical stability
Implement the glocal HMM; discard the extention HMM
Convert phredQ to probabilities
minor
prob_realn() seems working!
minor changes
this is interesting. multiplication is much faster than division, at least on my Mac
I was trying to accelerate ka_prob_glocal() as this will be the
round to the nearest integer
mark samtools-0.1.8-16 (r759)
* samtools-0.1.8-17 (r760)
I am changing the gap open probability back to 0.001. It seems that
* vcfutils.pl qstats: calculate marginal ts/tv
* samtools-0.1.8-18 (r763)
* removed a comment line in kaln.c
added filter for samtools/bcftools genetated VCFs
* vcfutils.pl: fixed a typo in help message
forget to add the key file
a minor change
* a minor fix to the -L option
improve the LD statistics
added another toy example
* Minor code changes. No real effect.
remove local realignment (probabilistic realignment is still there)
* samtools-0.1.8-19 (r777)
* samtools-0.1.8-20 (r778)
improve pileup a little bit
* samtools-0.1.8-21 (r780)
* samtools-0.1.8-22 (r781)
fixed a silly bug in pileup
Release samtools-0.1.9 (r783)
acknowledge Petr and John who have greatly contributed to the project.
Optionally output "DP", the individual read depth
* samtools-0.1.9-1 (r786)
* samtools-0.1.9-2 (r787)
Separate kaln and kprobaln as I am preparing further changes. At
fixed a minor problem in the example coming with kprobaln.c
for backup. no effective changes
* this revision is UNSTABLE
Revert to r790. The recent changes are not good...
prepare for the indel caller. It is not ready yet.
fixed a few bugs in the indel caller. Probably there are more.
indel calling is apparently working, but more information needs to be collected
* samtools-0.1.9-2 (r797)
Incorporate patches by Marcel Martin for read counting.
fixed a silly bug in the indel caller
fixed another silly bug in mpileup's indel caller
* samtools-0.1.9-4 (r801)
* samtools-0.1.9-5 (r802)
* samtools-0.1.9-6 (r803)
* samtools-0.1.9-7 (r804)
added a double-hit filter to avoid overestimated indel likelihood
bcftools: compute equal-tail (Bayesian) credible interval
* samtools-0.1.9-8 (r807)
minor change to makefile
* samtools-0.1.9-8 (r809)
* do not use reads containing too many mismatches for indel calling
use zlib for direct reading when BCF_LITE is in use
fixed a typo
* prepare to replace kaln with kprobaln in realignment
* samtools-0.1.9-9 (r810)
effectively revert to the viterbi version. The forward realignment gives too many false positives.
* samtools-0.1.9-10 (r816)
* samtools-0.1.19-11 (r817)
* samtools-r818
* samtools-0.1.9-13 (r819)
* samtools-0.1.9-14 (r820)
* samtools-0.1.9-15 (r821)
* samtools-0.1.9-16 (r822)
* samtools-0.1.9-r823
* samtools-0.1.9-17 (r824)
* samtools-0.1.9-18 (r825)
remove ZQ if both BQ and ZQ are present
bcftools: allow to skip indels
update version information: samtools-0.1.9-20 (r828)
Release samtools-0.1.10 (r829)
* samtools-0.1.10 (r831)
minor change to how seqQ is applied
fixed a bug in printing MNPs
* samtools-0.1.10-4 (r834)
* modify the filtering rule: also filter SNPs around filtered indels
* samtools-r836
Apply a patch by Rob Davis, which improves fault detection.
* samtools-0.1.10-6 (r839)
* samtools-0.1.10-4 (r840)
* samtools-0.1.10 (r841)
In merging, if -R is specified, do not abort if the sequence dictionary is different.
* samtools-0.1.10-9 (r844)
Release samtools-0.1.11
forget to change the version information
fixed a typo/bug in r^2 computation
* fixed a memory violation
fixed a memory leak in bam_fetch()
* samtools-0.1.11-1 (r858)
Release samtools-0.1.12
a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect
Release samtools-0.1.12a
more informative error message
* remove "-f". Instead always compute consensus quality
vcf->fastq
Fixed a compiling error when knetfile is not used.
bring back the windows support
In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
added a warning for the Windows version
fixed a bug in vcf2fq
* samtools-0.1.12-1 (r873)
a spelling error..
* samtools-0.1.12-2 (r877)
Make sure that the GT genotype field is the first
* fixed a minor issue in printing VCFs
drop bcf-fix.pl as it is redundant by the latest changes
compute max SP and max GQ from sample genotypes
* samtools-0.1.12-4 (r884)
(Arguably) improved the indel caller a tiny bit for lowCov data.
* samtools-0.1.12-6 (r887)
When -B is applied to mpileup, still use paired reads only unless -A is flagged.
* samtools-0.1.12-12 (r889)
* samtools-0.1.12-9 (r891)
added ST
sorry. It is SP not ST
* samtools-0.1.12-10 (r896)
move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
fixed two minor bugs in Fisher's exact test
* fixed a rare memory issue in bam_md.c
* avoid a segfault when network connect fails
* fixed an out-of-boundary bug
fixed a typo in the VCF header
finished VCF->BCF conversion
* automatically fix errors in GL
more meaningful BAM truncation message
added "const" to bcf_p1_cal()
added the phase command
update the BCF spec
* change the order of PL/GL according to the latest VCF spec
* put version number in bam.h
* 0.1.12-r924:126
minor changes to a heuristic rule
* optionally drop phase ambiguous reads
Release samtools-0.1.13 (r926:134)
added the haploid mode
export2sam.pl-2.3.1, provided by Chris Saunders from Illumina Inc.
* allow to change the compression level in BAM output
forget to add this file
Release samtools-0.1.14 (r933:170)
* added BED support to samtools view and mpileup and bcftools view
* synchronize bgzf in tabix and in samtools
Added an example of using mpileup
fixed a few typos in comments
added quality filtering
* added bam_verbose global variable
Release samtools-0.1.15 (r949:203)
* Added Brent's method for frequency estimate
* fixed a bug in bedidx: input BED not sorted
Added the support for the new SAM/BAM type "B"
fixed a bug in merge
Release samtools-0.1.16 (r963:234)
Removed the pileup command
* 0.1.16-dev (r969:252)
fixed a bug caused by a recent patch
Release samtools-0.1.17
fixed a bug in bam_plcmd.c
for WIN32 compatibility
support trio indels
subsampling read pairs
allow to set seed in view-subsampling
* bugfix in index: large memory when a read pos is 1
* Updated samtools to the latest
converted padded SAM to unpadded SAM
added the ace2sam converter
unpadded output
changes from git
bugfix: wrong SP; missing DV in the VCF header
Incoporated changes from Nils Homer.
Two auxilary Lua scripts
another example, used by g1k for QA
doc for downsampling
Removed SVN ChangeLog; merged my private github Log to ChangeLog.old
On behalf of Petr: multi-allelic GT
bugfix: downsampling not always working
On behalf of Bob Handsaker (5):
Fix problem with compiling without curses.
Pass LIBS to recursive targets to facilitate building at Broad.
Fix annoying segv when invalid region specified.
Introduced LIBPATH variable so this could be overridden to allow samtools to build correct at the Broad.
Change copyright notices now that MIT has approved open source distribution.
On behalf of John Marshall (20):
Return NULL from _razf_open() (and hence razf_open()/razf_open2())
Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
Index files should be opened in binary mode, not text mode.
Also clean *.exe (for Cygwin users using this makefile).
Put libraries at the end, so they can resolve references from libbam.a
Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
Depend on libbam.a rather than the phony target, so that samtools is not
Put the right filename in the error message.
Improve the invalid 'BAM\1' magic number error message, and also print it
Add svn:ignore properties listing the generated files.
Add svn:ignore properties for generated files that don't appear in "make all".
0 is a successful return value from bam_read1(). (In practice, it never
When bam_read1() returns an error (return value <= -2), propagate that error
Add bam_validate1().
Use bam_validate1() to detect garbage records in the event of a corrupt
Abort if merge -h's INH.SAM cannot be opened, just as we abort
Add the relevant filename or region to error messages, and cause a failure
When merging BAM headers, compare the list of target reference sequences
System libraries go *after* user libraries in link commands, because
Petr Danecek (34):
A bug fix, "samtools view" is now working again.
Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
Bug fix - faidx on RAZF compressed files now working.
Removed the offending knet_seek message.
Added the sam2vcf.pl script.
commit 56ae21c41704d35a30a642fb8a3ea9e39f6460b9
commit d410ecbf60b5aed90ee20c6ba40637ca50241edd
Now possible to merge multiple HeaderDict dictionaries
Added sam_header_line_free call for sam_header_parse2
Allow tabs in the CO header field
Small fix in VCF format: dot for the empty INFO field
Fixed a bug in knet_seek
Added VCF header
Added the -d option to limit maximum depth for indels.
Added possibility to specify a custom column title for the data column
Print an error for pileups in simple format
Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
Improved efficiency of header parsing
Added possibility to select indels only and fixed a bug in reporting homozygous indels.
Fixed the order of sequences in the header
Speedup with -i, no need to query the reference all the time
More descriptive message for space separated tags
Added the possibility to print or not to print the reference allele
Added a note about the indels coordinates
Initial release on behalf of Aylwyn Scally
Convert VCF output of "bcftools view -bgcv" to a valid VCF file
Added -b option: read file names from a file
Fixed the VCF header to pass validation
Fixed a typo in read_samples
Skip sites with unknown ref
Prevent division by zero
Initial release of bamcheck and plot-bamcheck
Added rule for bamcheck creation
Compile cleanly from top-level Makefile. Check for out of bounds tids.
peterjc (12):
Helpful error message on bad CIGAR in unpad_seq
Support CIGAR X/= in depad
Check current reference sequence matches RNAME in samtools depad
Cope with CIGAR D or P to mark gaps in an embedded padded reference
Add TODO note about reference lengths
Correct my error message; assed some comments
Record actual sequence in unpad_seq (fixes apparently harmless bug)
Include leading CIGAR P operators in 'samtools depad'
Tolerate CIGAR H operators in 'samtools depad'
Cope with leading CIGAR H (or H and S) in 'samtools depad'
Cope with trailing CIGAR H (or S and H) in 'samtools depad'
Check reference length in BAM header against embedded reference in 'samtools depad'
samtools (1):
Merge pull request #2 from peterjc/depad
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Processing of sequence alignments in SAM and BAM formats.
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