├── .github └── workflows │ └── docker-image.yml ├── .travis.yml ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── codecov.yml ├── deps ├── samtools-0.1.19.tar.bz2 └── samtools-1.6.tar.bz2 ├── docker └── amazon │ └── Dockerfile ├── install_deps.sh ├── run_tests.sh ├── sh ├── bam_annotate.sh ├── fastq2bam └── fastq_validator.sh ├── src ├── Makefile ├── bam2fastq.c ├── bam_add_tags.c ├── bam_umi_count.c ├── fastq.c ├── fastq.h ├── fastq_filter_n.c ├── fastq_filterpair.c ├── fastq_info.c ├── fastq_not_empty.c ├── fastq_num_reads.c ├── fastq_pre_barcodes.c ├── fastq_split_interleaved.c ├── fastq_tests.c ├── fastq_trim_poly_at.c ├── fastq_truncate.c ├── hash.c ├── hash.h ├── range_list.c ├── range_list.h └── sam_tags.h └── tests ├── 10xv1a_I1.fastq.gz ├── 10xv1a_R1.fastq.gz ├── 10xv1a_R2.fastq.gz ├── 10xv1a_R3.fastq.gz ├── a_1.fastq.bz2 ├── a_1.fastq.err.bz2 ├── a_1.fastq.gz ├── a_1.fastq.gz.bz2 ├── a_2.fastq.bz2 ├── a_2.fastq.gz ├── a_2.fastq.gz.bz2 ├── barcode_test2_1.fastq.gz ├── barcode_test2_2.fastq.gz ├── barcode_test_1.fastq.gz ├── barcode_test_2.fastq.gz ├── c18_10000_1.fastq.gz ├── c18_10000_1.fastq.gz.bz2 ├── c18_10000_2.fastq.gz ├── c18_10000_2.fastq.gz.bz2 ├── casava.1.8_1.fastq.gz ├── casava.1.8_2.fastq.gz ├── casava.1.8_readname_trunc_1.err.fastq.gz ├── casava.1.8_readname_trunc_1.err2.fastq.gz ├── casava.1.8_readname_trunc_1.fastq.gz ├── casava.1.8_readname_trunc_2.fastq.gz ├── casava.1.8i.fastq.gz ├── casava.1.8i_e1.fastq.gz ├── casava.1.8i_err.fastq.gz ├── check_no_dups.sh ├── inter.fastq.gz ├── known_cells.txt ├── known_umis.txt ├── mapTrans2Gene.tsv ├── nanopore_rna1.fastq.gz ├── nanopore_rna2.fastq.gz ├── nanopore_rna3.fastq.gz ├── nanopore_rna4.fastq.gz ├── nanopore_rna5.fastq.gz ├── no_qual.bam ├── one.fastq.gz ├── out_known_umis.txt ├── pbmc8k_S1_L007_R1_001.fastq.gz ├── pbmc8k_S1_L007_R2_001.fastq.gz ├── pe.bam ├── pe_bug14.fastq.gz ├── poly_at.fastq.gz ├── poly_at_len3.fastq.gz ├── pre1.fastq.gz ├── pre2.fastq.gz ├── pre3.fastq.gz ├── read-I1_si-ACCGAACA_lane-001-chunk-001.fastq.gz ├── read-I1_si-ACCGAACA_lane-001-chunk-001.fastq.gz.bz2 ├── read-I1_si-ACCGAACA_lane-002-chunk-000.fastq.gz ├── read-I1_si-AGGATCGA_lane-001-chunk-001.fastq.gz ├── read-I1_si-AGGATCGA_lane-002-chunk-000.fastq.gz ├── read-I2_si-ACCGAACA_lane-001-chunk-001.fastq.gz ├── read-I2_si-ACCGAACA_lane-001-chunk-001.fastq.gz.bz2 ├── read-I2_si-ACCGAACA_lane-002-chunk-000.fastq.gz ├── read-I2_si-AGGATCGA_lane-001-chunk-001.fastq.gz ├── read-I2_si-AGGATCGA_lane-002-chunk-000.fastq.gz ├── ref1.sam ├── rl_10.fastq.gz ├── se.bam ├── solexa_1.fastq.gz ├── solexa_2.fastq.gz ├── test.bam ├── test10.bam ├── test10e1.bam ├── test10e3.bam ├── test10e4.bam ├── test10e5.bam ├── test10e6.bam ├── test_1.fastq.gz ├── test_1.fastq_fix.fastq.gz ├── test_13.fastq.gz ├── test_17.fastq.gz ├── test_19.fastq.gz ├── test_2.fastq.gz ├── test_2.fastq_fix.fastq.gz ├── test_20.fastq.gz ├── test_21_1.fastq.gz ├── test_21_2.fastq.gz ├── test_22_1.fastq.gz ├── test_22_2.fastq.gz ├── test_30_1.fastq.gz ├── test_30_2.fastq.gz ├── test_33.fastq.gz ├── test_annot.bam ├── test_annot.mtx ├── test_annot2.bam ├── test_annot3_small.bam ├── test_annot4.bam ├── test_annot5.bam ├── test_dot.fastq.gz ├── test_dot.fastq_fix.fastq.gz ├── test_e1.fastq.gz ├── test_e10.fastq.gz ├── test_e11.fastq.gz ├── test_e12.fastq.gz ├── test_e13.fastq.gz ├── test_e14.fastq.gz ├── test_e15.fastq.gz ├── test_e16.fastq.gz ├── test_e17.fastq.gz ├── test_e19_1.fastq.gz ├── test_e19_2.fastq.gz ├── test_e2.fastq.gz ├── test_e20.fastq.gz ├── test_e21.fastq.gz ├── test_e3.fastq.gz ├── test_e4.fastq.gz ├── test_e5.fastq.gz ├── test_e6.fastq.gz ├── test_e7.fastq.gz ├── test_e8.fastq.gz ├── test_e9.fastq.gz ├── test_empty.fastq.gz ├── test_num.fastq.gz ├── test_one_cell.bam ├── test_ont.fastq.gz ├── test_ont2.fastq.gz ├── test_pacbio.fastq.gz ├── test_pacbio2.fastq.gz ├── test_solid2_1.fastq.gz ├── test_solid2_2.fastq.gz ├── test_solid_1.fastq.gz ├── test_solid_2.fastq.gz ├── trans.bam ├── 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