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N!p= ף?8E Eb Eb Eb E1 E E E O O OO;OIbP (" QX" [ samtools/usr/include/bits/usr/include/usr/lib/gcc/x86_64-linux-gnu/4.4.5/include/usr/include/syssam_view.c.pysam.ckhash.hstdio2.hstdio.hstring3.hstdlib.hkstring.hstddef.htypes.hstdio.hlibio.htypes.hstdint.hknetfile.hbgzf.hbam.hsam.hpysam.hgetopt.h  <=}x}X~<~X~JXfܔ"=WYXnf}.}X==}<=e^"^X#=K:WK=q]WJ)W<*XZ)RJ.<R</ZO1<O<2==:=c^T02\X/;'7s$gH0d}}JX}fE;J=DJ?A>=I=}.J}',Y0L< x+4tJ=<>=I=}.J}',Y8D x#>tw. <w. <w. <w. <w  X vttw.to oa'~1gy./y.~J~Xwg[wtgZ$w[ gxXY XfXKud<hבrXp<XpX1~J~tf6~<t}}cX}JK=~N3%JJq;=givIK:JK}r=^,惁 J"KJXɄ[9:hXXIK=~f#M!X~%u~#:C=:m=:ZLX}JR=}M"Z#<tfGX>"K~&EKI=}.J}f*!;=k ȃY;ws%~.~.~.3XL* ׭x%<>f9?~."o!u1Y Options: -b output BAM -r/1/2+RGbxXh%s@RG ID:standard output%d import-o-btUsage: samtools view [options] | [region1 [...]] -h print header for the SAM output -H print header only (no alignments) -S input is SAM -u uncompressed BAM output (force -b) -1 fast compression (force -b) -x output FLAG in HEX (samtools-C specific) -X output FLAG in string (samtools-C specific) -c print only the count of matching records -L FILE output alignments overlapping the input BED FILE [null] -t FILE list of reference names and lengths (force -S) [null] -T FILE reference sequence file (force -S) [null] -o FILE output file name [stdout] -R FILE list of read groups to be outputted [null] -f INT required flag, 0 for unset [0] -F INT filtering flag, 0 for unset [0] -q INT minimum mapping quality [0] -l STR only output reads in library STR [null] -r STR only output reads in read group STR [null] -s FLOAT fraction of templates to subsample; integer part as seed [-1] -? longer help Notes: 1. By default, this command assumes the file on the command line is in the BAM format and it prints the alignments in SAM. If `-t' is applied, the input file is assumed to be in the SAM format. The file supplied with `-t' is SPACE/TAB delimited with the first two fields of each line consisting of the reference name and the corresponding sequence length. The `.fai' file generated by `faidx' can be used here. This file may be empty if reads are unaligned. 2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'. 3. BAM->SAM conversion: `samtools view in.bam'. 4. A region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is specified, the input alignment file must be an indexed BAM file. 5. Option `-u' is preferred over `-b' when the output is piped to another samtools command. 6. In a string FLAG, each character represents one bit with p=0x1 (paired), P=0x2 (properly paired), u=0x4 (unmapped), U=0x8 (mate unmapped), r=0x10 (reverse), R=0x20 (mate reverse) 1=0x40 (first), 2=0x80 (second), s=0x100 (not primary), f=0x200 (failure) and d=0x400 (duplicate). Note that `-x' and `-X' are samtools-C specific. Picard and older samtools do not support HEX or string flags. Usage: samtools bam2fq Sbct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:[main_samview] fail to open "%s" for reading. [main_samview] fail to read the header from "%s". [main_samview] fail to open "%s" for writing. [main_samview] truncated file. [main_samview] random alignment retrieval only works for indexed BAM files. [main_samview] region "%s" specifies an unknown reference name. Continue anyway. [main_samview] retrieval of region "%s" failed due to truncated file or corrupt BAM index file Usage: bamtk import  5a 0`   0 ` Y0`V-?P?p= ף??wwww  w( w0w8w;U;VUVT\T\!FRRR$S$a_an]n~R]_]__]T !w!2w26w6ew @U@dVprwrtwtvwvxw xyw(yzw0z~w8~TwpU#9UpT;T#6T_Lh_i_#_ViV#V^ir^r~Q~PQP^T^#^P/Z:KPKnZ#ZhShyPSSiS#SUPUfiUPPP#U PUfiUR`{w{W w0`USUW S`TPP P' H PL O PU2UU UR8RR R,[PP  P` { w{ G w0` U S U G S` T P P P 8 P< ? 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