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Changeset 1:59eca98715b4 (2015-12-21)

Previous changeset 0:c91df5df0faf (2015-12-21) Next changeset 2:7ec666e2f315 (2015-12-21)

Commit message:
Deleted selected files

removed:
test-data/in_short.sam

diff -r c91df5df0faf -r 59eca98715b4 test-data/in_short.sam
--- a/test-data/in_short.sam Mon Dec 21 07:12:34 2015 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b"@@ -1,10000 +0,0 @@\n-@SQ\tSN:gi|15829254|ref|NC_002695.1|\tLN:5498450\n-@RG\tID:test_sample\tSM:test_sample\n-@PG\tID:bwa\tPN:bwa\tVN:0.7.12-r1039\tCL:bwa mem -R @RG\\tID:test_sample\\tSM:test_sample -t 1 ref.fa r1.fastq r2.fastq\n-HWI-D00151:47:H7926ADXX:1:1101:1645:2045\t83\tgi|15829254|ref|NC_002695.1|\t5459580\t60\t100M\t=\t5459536\t-144\tGCATCGGGTTGCCAGTCCGGATACATGGCGAATTTCCCCATGGGTACAGCAACGGGAGCGGCTTGCGGTTCCTGATAGAGTTGATCGTCCAGATCGACAN\tFFFBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFBFFFFFBFFFFFFFFFFFFIIIIIIIIIFFIIIIIIIIIIIFIFIIIIIIFIIFFFFFFFFFB<0#\tNM:i:1\tMD:Z:99T0\tAS:i:99\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:1645:2045\t163\tgi|15829254|ref|NC_002695.1|\t5459536\t60\t100M\t=\t5459580\t144\tCTCTTAGCGCCACGCCCCATAGAGCCGCCAGGCGGATAAAGTCGGCATCGGGTTGCCAGTCCGGATACATGGCGAATTTCCCCATGGGTACAGCAACGGG\tBBBFFFFFFFFFFFFIIIIIFIIIIIFIIIFIFFIBFFFFFFFFBFBBBBFFFBFBFFFFFFFFBBBFBBFFBFBFFFFFFFFBBFBFBFFBBBBBBBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:1584:2047\t83\tgi|15829254|ref|NC_002695.1|\t1794502\t60\t100M\t=\t1794386\t-216\tGAAATTATTAGCACCACAGTCAGTTTGTGAAAATGTGAAGATATTCAGAAGTTTTATTCAGTCATGATACAGGCATCCTCCGGGATGCCTGTTGTTTTTN\tBFFFFBBBFFFFFFFFFFFFFFBFFFFFFFFFFFFFIIIIIIIIIFIFIIIFIIIIIFIIIIFBIIFFFFFBIIIFIFBIIIIIIIIFFFFFFFFFF<0#\tNM:i:1\tMD:Z:99G0\tAS:i:99\tXS:i:37\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:1584:2047\t163\tgi|15829254|ref|NC_002695.1|\t1794386\t60\t96M\t=\t1794502\t216\tGGGCGGCAGAGGGAAAAAGAATAAAAAAATCCCGCAGAGTTGCGGGGACAGACAAAGATTAACGTTAAGGAGGTATTTTTGTTTCTGGTGCTCGGG\tB<BFFFBBFFFF'0BFFFFFFBFFFIIIFIFFFFFFFBB'<BBBBB<777<7770<B<<<<<'77007<BB<0<<<FFFBB<BB0<<B<<'00<<B\tNM:i:2\tMD:Z:12T59T23\tAS:i:86\tXS:i:22\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:1733:2205\t83\tgi|15829254|ref|NC_002695.1|\t3503961\t60\t100M\t=\t3503681\t-380\tAACACATTGTCTGCCACGTGATTGTGGATGGAGAATGCACCTTCACTATTCGTACCGCTCACCGTCGTACCGTTAGTGTTAGTTTTTAAAATTGCACCAT\tFFFBFFBFFFFFFFFFFFFFFBBFFFBFFFFFFFFFFFFFFFFFFFFFFFFIFFIIFIFFFIFIFIIFFIIIIIIIIIFIIIIIIFFFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:1733:2205\t163\tgi|15829254|ref|NC_002695.1|\t3503681\t60\t100M\t=\t3503961\t380\tGGATATAATTGTTGTGTCAGCTTTCCCGCCGCTTTTGATATTTTGCGTTCCGCTGTTGATATTGGTGCCTGTGGCTATGCCATAATTATTAATATTCTGT\tBBBFFFFFFFFFFIIIIIIIIFIIIIIIIIIIIIIIIFIIIIIIIIIIIFFFIIFFFFBFFFFFFFBFFFFFFFFFFFFFBBBFFFFFFFFBFBBFFFFF\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:2088:2189\t99\tgi|15829254|ref|NC_002695.1|\t1652878\t60\t100M\t=\t1653052\t274\tCTGTAGATCTGGAAATCGCAACGGAGGAAGAAACCTCATTGCTGGAAGCCTGGAAAAAGTATCGGGTGTTGCTGAACCGTGTTGATACATCAACTGCACC\t7BBBFFFFFFFFFFIFIIIIFFFIFIFFBFBFBFFFFFFFIIIIFBBFIIFIFIIFBFFBBFBBBFBBBBBFFFBBBFFBB<BBFFBBFFBBBFFFFFFB\tNM:i:1\tMD:Z:32G67\tAS:i:95\tXS:i:86\tRG:Z:test_sample\tXA:Z:gi|15829254|ref|NC_002695.1|,-3476634,100M,3;\n-HWI-D00151:47:H7926ADXX:1:1101:2088:2189\t147\tgi|15829254|ref|NC_002695.1|\t1653052\t60\t100M\t=\t1652878\t-274\tAATGTATTTTCAGAGGCTAGAGCTTAGGATATCTCAGCGGCAATTAACTTATGAGGGATAGCTAAATACCAGAAGATAATTAGTTTTTACTATTTATCTT\tFFBBBBBBBBFBFFFB<FFFFFFBIFFBFFFBF7FFIIIFFFFIFFBIIIIIIIFFFFFIIIFFBFFBIIIIIIIIFFIFFIIIIFFFBFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:2359:2127\t99\tgi|15829254|ref|NC_002695.1|\t1862580\t60\t100M\t=\t1862674\t194\tGCGTTAATTAACCAGCGCCCTAAACCCGGCCAGCTAAAAACCATTTCGGTGATCATCGCCAGCGTCAGCATGGTGGAAAACTGTAAGCCCAGGCGAGGAA\tBBBFFFFFFFFFFIFFFIIFIIFBFFFFBFFFIIIFIIIIBFIIIIIBBFFFFFFFFFFFFFBFFFFBFFFFF<BFBBBFFFFFFFFFFFFFFFFFFFFB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:2359:2127\t147\tgi|15829254|ref|NC_002695.1|\t1862674\t60\t100M\t=\t1862580\t-194\tGAGGAATACCCGGCGGTAACGCGTTATGCAGAACGTGGCGACGCAAAATAGTAAAGCGCGACAAACCGCGGGTCGCCGCCGCTTTTACATAGTTCTGGTC\tFFFFFB<0'<<BFFFB<77<BBBFBFBFFBBB<BFFFBB7'BBBFFB<BBBBFBBB77BBBBB<<FBFBFFFFFFIF<IIIIIIIIFFFFFFFFFFFBBB\tNM:i:1\tMD:Z:8A91\tAS:i:95\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:2473:2147\t99\tgi|15829254|ref|NC_002695.1|\t2921256\t40\t100M\t=\t2921378\t222\tGGGAAACCCTGTCCAGCAACTGCAGGAACCAGTAGCCCGTTCCCACCGCTGACGTGGTGTATGACAC"..b"BBFFFFIIFIIIIFFFIIFIIFBBFFFFFFFBBBBBBBBBB<<BBBBBBBFBBFBBBBBBBBBBBBBBB<BBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:6072:14609\t147\tgi|15829254|ref|NC_002695.1|\t3592550\t60\t77M\t=\t3592174\t-453\tACGGTATGAGCAATGGCATTTTTGCCCGGTTCGGCACGTTTCATAGTATCGCGCACTGGTGCGGCTAGGATCCCTCC\tB77'<BB<<0<<00<'BBB77B<<770<7B7BFB<0BBFBB7BFFFBFFB7FBFBFIIFFBBFFBBFFF<B7<F0<B\tNM:i:0\tMD:Z:77\tAS:i:77\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:6140:14618\t99\tgi|15829254|ref|NC_002695.1|\t217729\t60\t100M\t=\t217827\t198\tACCCTTCAGAAACCCAGGAGCGTATGATGCTGCGCCTGCTGGCGTGGCTGAAATATGCTGATGAACGTCTGCAATTTACCCGTGGTTTGTGTGCCGATGA\tBBBFFFFFFFFFFIIIIIFFFIFIIIIIIIIIIIIIIIIIIIIIIIIFIIFFFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFBFFBBFFBFFFFBFFFFF\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:6140:14618\t147\tgi|15829254|ref|NC_002695.1|\t217827\t60\t100M\t=\t217729\t-198\tGATGAGCCGGAAGCGTGGCTGCGTAACGATCACCTGGGCATTGATTTGTGGATTGAGCTGGGGCTGCCGGATGAGCGACGAATTAAGAAAGCCTGCACCC\tFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFB<FFFFFFFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:6059:14667\t99\tgi|15829254|ref|NC_002695.1|\t1826409\t60\t100M\t=\t1826576\t267\tTCACGGTACTCTACCGTTGGCCTCACTCGTTACTTAGCAATGCCCCGGCTCCACAAACGACGAATATTTTCAGCCATCTTCTTTTACCCTCCACGTCATC\tBBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:6059:14667\t147\tgi|15829254|ref|NC_002695.1|\t1826576\t60\t100M\t=\t1826409\t-267\tCAATTTACGTCGGTAGATGTTTTACGGATGCAGAAATTTTATCTGCCGCGTAAAAAGTCTTCGTTTTACCGGCCTGATACTTTTTTGCAATGGGGTGGAC\tFFFFFB<FBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFBBBFFFFFFFIIIIIIIIIIIIIIIIIIFFIIIIIIIIIFFIFIIIIIIFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:6354:14617\t83\tgi|15829254|ref|NC_002695.1|\t3190027\t60\t100M\t=\t3189766\t-361\tTGAAGATCCAAGTTTTATCTTCGATAAAATATCACACAAACTCAGACATACGGTAACGGAATTCGATGAGAGCGGGAAAAGCGAACCAACGGGCTTATTT\tBB<BB<BBFBFFFFFFBBFFFFFFFFFBFB<BBBBFFBBBBBFFFFFFFBIIIIFFIIIFBBBB<FBFIIIFFFIIIIFIFFFFFFFFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:6354:14617\t163\tgi|15829254|ref|NC_002695.1|\t3189766\t60\t100M\t=\t3190027\t361\tTGACAACATAGTTGAGAAGACTCATGATGATATAAATAATGCTGAATTTACTGATGGTGGTATTGATGATCGTAGTGATATTGGCATTGACTCCAATGAT\tB<BFBFBFFFBFBF<<FBFFII<FFI0BB<B7B0FFFFFIFBBFF<FFFFFBFBFFI7BF7B<BF<FFFFFI77<<BBB<BBFFFB<BBF0BBB<<B<BB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:6396:14642\t83\tgi|15829254|ref|NC_002695.1|\t5190286\t60\t100M\t=\t5190150\t-236\tTGCAGTAGAGGAAGGCAATGGTAGTAACCGCCAGATATGCCGGGCGTGCTTTACCAAAGTGACCGTGTCCGAGCAGCAGTAACGCCGCACAGGTGTAAAG\tFFFFBFFFFFFFFFFFFFFFFFFFBBBFBBBFFFFBBFBBBFFFFFFFFFFFBFFFFFFFIIIIIFIIFFFBFFFFFFIIFIFFFFFFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:6396:14642\t163\tgi|15829254|ref|NC_002695.1|\t5190150\t60\t100M\t=\t5190286\t236\tTTGCTTATTGGTGCATCTAAGGGATACGGGTTTTTATGCAGCCGGTTGTAATTCAGCGCATACATGGCGGTGATGACCATCAGGGTGACAAATGACCACA\tBBBFFFFFBFFFFIFFFIIIFIIFFFIIIIBFFFIFFFFFBFFIIFFFFFFIIIIBFIFBBFFFFFFBFB<B7<07<<BBBBBBB7B0<BFBB<0'<<7B\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:7030:14541\t99\tgi|15829254|ref|NC_002695.1|\t3843633\t60\t100M\t=\t3843936\t403\tCCTTCCGGGAATCGCCATGCCACCGAAAATCCTAATTCCTGGAATTCGTCGATGTGCATTTTTTTACGCAGACGACGGCTACGGTTCTTTGCCATTATTT\tBBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIFFIFFFIIIIIIIFFFFFIFFFBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n-HWI-D00151:47:H7926ADXX:1:1101:7030:14541\t147\tgi|15829254|ref|NC_002695.1|\t3843936\t60\t100M\t=\t3843633\t-403\tGCTGCAGTTTGCTTTTTACCAGTTCGGCAAACGGCACCTGAACGATACGGCGTTTATTATGGCGCGCTTTGTGCCACGGGTCAGGGAAAAAGAGCTGCAC\tFFFFFFFFFFFFFFFFBBBFFFFBFFFFFFBFFBBBBBFFBBFBBBFFFFFIIIIFIIIIIFIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFFFFFBBB\tNM:i:0\tMD:Z:100\tAS:i:100\tXS:i:0\tRG:Z:test_sample\n"